dbSNP rs12449210: HYDIN:c.-82A>T (chr16-71230620-T-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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

GnomAD3 exomes

AF:

0.400

AC:

54708

AN:

136730

Hom.:

11809

AF XY:

0.391

AC XY:

29013

AN XY:

74238

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 SAS exome

AF:

0.375

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

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.558

Gnomad4 ASJ exome

AF:

0.351

Gnomad4 EAS exome

AF:

0.553

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.282

Gnomad4 NFE exome

AF:

0.321

Gnomad4 OTH exome

AF:

0.352

GnomAD4 genome

AF:

0.349

AC:

52968

AN:

151894

Hom.:

9703

Cov.:

AF XY:

0.349

AC XY:

25872

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.335

Gnomad4 AMR

AF:

0.463

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.573

Gnomad4 SAS

AF:

0.382

Gnomad4 FIN

AF:

0.265

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.330

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

DANN

Benign

0.87

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over