Variant rs2837170 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080444.2(IGSF5):c.101-7014C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 151,990 control chromosomes in the GnomAD database, including 50,824 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.82 ( 50824 hom., cov: 31)

Consequence

IGSF5
NM_001080444.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60

Variant links:

Genes affected

IGSF5 (HGNC:5952): (immunoglobulin superfamily member 5) Predicted to enable PDZ domain binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be located in apical plasma membrane. Predicted to be integral component of membrane. Predicted to be active in bicellular tight junction and cell surface. [provided by Alliance of Genome Resources, Apr 2022]

IGSF5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGSF5	NM_001080444.2 link	c.101-7014C>A		intron_variant		ENST00000380588.5	NP_001073913.1	Q9NSI5
IGSF5	XM_047440699.1 link	c.371-7014C>A		intron_variant			XP_047296655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGSF5	ENST00000380588.5 link	c.101-7014C>A		intron_variant		1	NM_001080444.2	ENSP00000369962.4		Q9NSI5
IGSF5	ENST00000479378.1 link	n.207-7014C>A		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.816

AC:

123980

AN:

151872

Hom.:

50784

Cov.:

show subpopulations

Gnomad AFR

AF:

0.785

Gnomad AMI

AF:

0.827

Gnomad AMR

AF:

0.859

Gnomad ASJ

AF:

0.735

Gnomad EAS

AF:

0.681

Gnomad SAS

AF:

0.807

Gnomad FIN

AF:

0.836

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.838

Gnomad OTH

AF:

0.802

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.816

AC:

124079

AN:

151990

Hom.:

50824

Cov.:

AF XY:

0.815

AC XY:

60521

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.784

Gnomad4 AMR

AF:

0.859

Gnomad4 ASJ

AF:

0.735

Gnomad4 EAS

AF:

0.682

Gnomad4 SAS

AF:

0.808

Gnomad4 FIN

AF:

0.836

Gnomad4 NFE

AF:

0.838

Gnomad4 OTH

AF:

0.800

Alfa

AF:

0.828

Hom.:

67050

Bravo

AF:

0.817

Asia WGS

AF:

0.754

AC:

2623

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.46

DANN

Benign

0.49

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over