dbSNP rs4788770: HYDIN:p.Asp359Asp (chr16-71129790-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001270974.2(HYDIN):c.1077T>C(p.Asp359Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,584,486 control chromosomes in the GnomAD database, including 31,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 3298 hom., cov: 30)

Exomes 𝑓: 0.28 ( 27788 hom. )

Consequence

HYDIN
NM_001270974.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.70

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 16-71129790-A-G is Benign according to our data. Variant chr16-71129790-A-G is described in ClinVar as [Benign]. Clinvar id is 402957.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.7 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HYDIN	NM_001270974.2 link	c.1077T>C	p.Asp359Asp	synonymous_variant	Exon 9 of 86	ENST00000393567.7	NP_001257903.1	Q4G0P3-1
HYDIN	NM_017558.5 link	c.1077T>C	p.Asp359Asp	synonymous_variant	Exon 9 of 20		NP_060028.2	Q4G0P3-5
HYDIN	NM_001198542.1 link	c.1158T>C	p.Asp386Asp	synonymous_variant	Exon 9 of 19		NP_001185471.1	Q4G0P3-8
HYDIN	NM_001198543.1 link	c.1128T>C	p.Asp376Asp	synonymous_variant	Exon 9 of 19		NP_001185472.1	Q4G0P3-10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HYDIN	ENST00000393567.7 link	c.1077T>C	p.Asp359Asp	synonymous_variant	Exon 9 of 86	5	NM_001270974.2	ENSP00000377197.2		Q4G0P3-1

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

43443

AN:

149160

Hom.:

3287

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.284

GnomAD3 exomes

AF:

0.336

AC:

71275

AN:

212204

Hom.:

10052

AF XY:

0.329

AC XY:

37756

AN XY:

114780

show subpopulations

Gnomad AFR exome

AF:

0.305

Gnomad AMR exome

AF:

0.525

Gnomad ASJ exome

AF:

0.326

Gnomad EAS exome

AF:

0.510

Gnomad SAS exome

AF:

0.341

Gnomad FIN exome

AF:

0.230

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.277

AC:

397009

AN:

1435208

Hom.:

27788

Cov.:

AF XY:

0.278

AC XY:

198395

AN XY:

714000

show subpopulations

Gnomad4 AFR exome

AF:

0.297

Gnomad4 AMR exome

AF:

0.472

Gnomad4 ASJ exome

AF:

0.318

Gnomad4 EAS exome

AF:

0.457

Gnomad4 SAS exome

AF:

0.330

Gnomad4 FIN exome

AF:

0.232

Gnomad4 NFE exome

AF:

0.258

Gnomad4 OTH exome

AF:

0.295

GnomAD4 genome

AF:

0.291

AC:

43490

AN:

149278

Hom.:

3298

Cov.:

AF XY:

0.291

AC XY:

21226

AN XY:

72862

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.389

Gnomad4 ASJ

AF:

0.308

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.331

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.300

Hom.:

779

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 02, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.31

DANN

Benign

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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