Variant chrX-131274771-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001555.5(IGSF1):c.3579C>T(p.Val1193=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,208,393 control chromosomes in the GnomAD database, including 34,544 homozygotes. There are 107,036 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 4060 hom., 10057 hem., cov: 22)

Exomes 𝑓: 0.26 ( 30484 hom. 96979 hem. )

Consequence

IGSF1
NM_001555.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.731

Variant links:

Genes affected

IGSF1 (HGNC:5948): (immunoglobulin superfamily member 1) This gene encodes a member of the immunoglobulin-like domain-containing superfamily. Proteins in this superfamily contain varying numbers of immunoglobulin-like domains and are thought to participate in the regulation of interactions between cells. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]

IGSF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant X-131274771-G-A is Benign according to our data. Variant chrX-131274771-G-A is described in ClinVar as [Benign]. Clinvar id is 257592.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-131274771-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGSF1	NM_001555.5 linkuse as main transcript	c.3579C>T	p.Val1193=	synonymous_variant	18/20	ENST00000361420.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGSF1	ENST00000361420.8 linkuse as main transcript	c.3579C>T	p.Val1193=	synonymous_variant	18/20	1	NM_001555.5	P4	Q8N6C5-1

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

33026

AN:

110535

Hom.:

4064

Cov.:

AF XY:

0.306

AC XY:

10033

AN XY:

32813

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.820

Gnomad SAS

AF:

0.443

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.313

GnomAD3 exomes

AF:

0.350

AC:

64209

AN:

183457

Hom.:

9446

AF XY:

0.337

AC XY:

22855

AN XY:

67895

show subpopulations

Gnomad AFR exome

AF:

0.350

Gnomad AMR exome

AF:

0.527

Gnomad ASJ exome

AF:

0.259

Gnomad EAS exome

AF:

0.827

Gnomad SAS exome

AF:

0.431

Gnomad FIN exome

AF:

0.243

Gnomad NFE exome

AF:

0.223

Gnomad OTH exome

AF:

0.309

GnomAD4 exome

AF:

0.263

AC:

289224

AN:

1097802

Hom.:

30484

Cov.:

AF XY:

0.267

AC XY:

96979

AN XY:

363248

show subpopulations

Gnomad4 AFR exome

AF:

0.355

Gnomad4 AMR exome

AF:

0.517

Gnomad4 ASJ exome

AF:

0.258

Gnomad4 EAS exome

AF:

0.816

Gnomad4 SAS exome

AF:

0.421

Gnomad4 FIN exome

AF:

0.239

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.297

GnomAD4 genome

AF:

0.299

AC:

33037

AN:

110591

Hom.:

4060

Cov.:

AF XY:

0.306

AC XY:

10057

AN XY:

32879

show subpopulations

Gnomad4 AFR

AF:

0.345

Gnomad4 AMR

AF:

0.415

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.821

Gnomad4 SAS

AF:

0.443

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.219

Gnomad4 OTH

AF:

0.315

Alfa

AF:

0.248

Hom.:

13562

Bravo

AF:

0.323

EpiCase

AF:

0.222

EpiControl

AF:

0.225

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

X-linked central congenital hypothyroidism with late-onset testicular enlargement

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.31

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.31

Position offset: -5

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