rs12449210

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001270974.2(HYDIN):c.-82A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 1,535,590 control chromosomes in the GnomAD database, including 91,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 9703 hom., cov: 32)

Exomes 𝑓: 0.34 ( 81516 hom. )

Consequence

HYDIN
NM_001270974.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0750

Publications

10 publications found

Variant links:

Genes affected

HYDIN (HGNC:19368): (HYDIN axonemal central pair apparatus protein) This gene encodes a protein that may be involved in cilia motility. Mutations in this gene cause of autosomal recessive primary ciliary dyskinesia-5, a disorder characterized by the accumulation of cerebrospinal fluid within the ventricles of the brain. A duplicate copy of this gene has been found in humans on chromosome 1. [provided by RefSeq, Jan 2013]

HYDIN Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 5
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, ClinGen, G2P
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

HYDIN links:

ENSG00000297892 (HGNC:):

ENSG00000297892 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 16-71230620-T-A is Benign according to our data. Variant chr16-71230620-T-A is described in ClinVar as Benign. ClinVar VariationId is 402959.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
HYDIN	NM_001270974.2 link	c.-82A>T	5_prime_UTR_variant	Exon 1 of 86	ENST00000393567.7	NP_001257903.1	Q4G0P3-1
HYDIN	NM_017558.5 link	c.-82A>T	5_prime_UTR_variant	Exon 1 of 20		NP_060028.2	Q4G0P3-5
HYDIN	NM_001198542.1 link	c.58+10A>T	intron_variant	Intron 1 of 18		NP_001185471.1	Q4G0P3-8
HYDIN	NM_001198543.1 link	c.28+40A>T	intron_variant	Intron 1 of 18		NP_001185472.1	Q4G0P3-10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HYDIN	ENST00000393567.7 link	c.-82A>T		5_prime_UTR_variant	Exon 1 of 86	5	NM_001270974.2	ENSP00000377197.2		Q4G0P3-1

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52884

AN:

151774

Hom.:

9673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.462

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.573

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.325

GnomAD2 exomes

AF:

0.400

AC:

54708

AN:

136730

AF XY:

0.391

show subpopulations

Gnomad AFR exome

AF:

0.330

Gnomad AMR exome

AF:

0.570

Gnomad ASJ exome

AF:

0.351

Gnomad EAS exome

AF:

0.594

Gnomad FIN exome

AF:

0.278

Gnomad NFE exome

AF:

0.328

Gnomad OTH exome

AF:

0.373

GnomAD4 exome

AF:

0.337

AC:

466950

AN:

1383696

Hom.:

81516

Cov.:

AF XY:

0.338

AC XY:

230883

AN XY:

682790

show subpopulations

African (AFR)

AF:

0.338

AC:

10685

AN:

31594

American (AMR)

AF:

0.558

AC:

19915

AN:

35690

Ashkenazi Jewish (ASJ)

AF:

0.351

AC:

8835

AN:

25180

East Asian (EAS)

AF:

0.553

AC:

19762

AN:

35722

South Asian (SAS)

AF:

0.377

AC:

29873

AN:

79228

European-Finnish (FIN)

AF:

0.282

AC:

9554

AN:

33894

Middle Eastern (MID)

AF:

0.302

AC:

1720

AN:

5696

European-Non Finnish (NFE)

AF:

0.321

AC:

346229

AN:

1078800

Other (OTH)

AF:

0.352

AC:

20377

AN:

57892

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

17036

34072

51108

68144

85180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11534

23068

34602

46136

57670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.349

AC:

52968

AN:

151894

Hom.:

9703

Cov.:

AF XY:

0.349

AC XY:

25872

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.335

AC:

13877

AN:

41420

American (AMR)

AF:

0.463

AC:

7071

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1212

AN:

3466

East Asian (EAS)

AF:

0.573

AC:

2953

AN:

5154

South Asian (SAS)

AF:

0.382

AC:

1842

AN:

4816

European-Finnish (FIN)

AF:

0.265

AC:

2790

AN:

10542

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.327

AC:

22189

AN:

67920

Other (OTH)

AF:

0.330

AC:

696

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1696

3392

5087

6783

8479

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.250

Hom.:

872

Bravo

AF:

0.366

Asia WGS

AF:

0.478

AC:

1658

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Primary ciliary dyskinesia 5

Benign:1

Aug 10, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

6.7

(source)

DANN

Benign

0.87

PhyloP100

-0.075

PromoterAI

0.035

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over