Variant chr22-26484040-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001013694.3(SRRD):c.150C>T(p.Gly50=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00478 in 1,336,880 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0050 ( 31 hom. )

Consequence

SRRD
NM_001013694.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.643

Variant links:

Genes affected

SRRD (HGNC:33910): (SRR1 domain containing) Predicted to be involved in microtubule-based process; regulation of circadian rhythm; and regulation of heme biosynthetic process. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SRRD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 22-26484040-C-T is Benign according to our data. Variant chr22-26484040-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3238993.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.643 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 31 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SRRD	NM_001013694.3 linkuse as main transcript	c.150C>T	p.Gly50=	synonymous_variant	1/7	ENST00000215917.11
SRRD	XM_017028799.3 linkuse as main transcript	c.150C>T	p.Gly50=	synonymous_variant	1/6
SRRD	XM_011530178.3 linkuse as main transcript	c.-110C>T		5_prime_UTR_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRRD	ENST00000215917.11 linkuse as main transcript	c.150C>T	p.Gly50=	synonymous_variant	1/7	1	NM_001013694.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00307

AC:

422

AN:

137292

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00279

Gnomad ASJ

AF:

0.00546

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00230

Gnomad FIN

AF:

0.000236

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00483

Gnomad OTH

AF:

0.00158

GnomAD3 exomes

AF:

0.00484

AC:

364

AN:

75232

Hom.:

AF XY:

0.00482

AC XY:

208

AN XY:

43194

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00213

Gnomad ASJ exome

AF:

0.0269

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00134

Gnomad FIN exome

AF:

0.000445

Gnomad NFE exome

AF:

0.00480

Gnomad OTH exome

AF:

0.00325

GnomAD4 exome

AF:

0.00497

AC:

5967

AN:

1199456

Hom.:

Cov.:

AF XY:

0.00494

AC XY:

2922

AN XY:

591126

show subpopulations

Gnomad4 AFR exome

AF:

0.000959

Gnomad4 AMR exome

AF:

0.00233

Gnomad4 ASJ exome

AF:

0.0171

Gnomad4 EAS exome

AF:

0.0000497

Gnomad4 SAS exome

AF:

0.00115

Gnomad4 FIN exome

AF:

0.000636

Gnomad4 NFE exome

AF:

0.00539

Gnomad4 OTH exome

AF:

0.00470

GnomAD4 genome

AF:

0.00307

AC:

422

AN:

137424

Hom.:

Cov.:

AF XY:

0.00272

AC XY:

181

AN XY:

66506

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00278

Gnomad4 ASJ

AF:

0.00546

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00230

Gnomad4 FIN

AF:

0.000236

Gnomad4 NFE

AF:

0.00483

Gnomad4 OTH

AF:

0.00156

Alfa

AF:

0.00452

Hom.:

Bravo

AF:

0.00340

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2024

SRRD: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

5.5

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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