Variant 2-172446825-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001394928.1(ITGA6):c.183-18714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 152,266 control chromosomes in the GnomAD database, including 366 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 366 hom., cov: 32)

Consequence

ITGA6
NM_001394928.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.286

Variant links:

Genes affected

ITGA6 (HGNC:6142): (integrin subunit alpha 6) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function in cell surface adhesion and signaling. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 6 subunit. This subunit may associate with a beta 1 or beta 4 subunit to form an integrin that interacts with extracellular matrix proteins including members of the laminin family. The alpha 6 beta 4 integrin may promote tumorigenesis, while the alpha 6 beta 1 integrin may negatively regulate erbB2/HER2 signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

ITGA6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 2-172446825-A-G is Benign according to our data. Variant chr2-172446825-A-G is described in ClinVar as [Benign]. Clinvar id is 1599744.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA6	NM_000210.4 linkuse as main transcript	c.183-18714A>G		intron_variant		ENST00000684293.1	NP_000201.2
ITGA6	NM_001394928.1 linkuse as main transcript	c.183-18714A>G		intron_variant		ENST00000442250.6	NP_001381857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA6	ENST00000442250.6 linkuse as main transcript	c.183-18714A>G		intron_variant		5	NM_001394928.1	ENSP00000406694		P23229-1
ITGA6	ENST00000684293.1 linkuse as main transcript	c.183-18714A>G		intron_variant			NM_000210.4	ENSP00000508249	P3	P23229-2

Frequencies

GnomAD3 genomes

AF:

0.0524

AC:

7967

AN:

152148

Hom.:

366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0121

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0563

Gnomad ASJ

AF:

0.0444

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.0896

Gnomad FIN

AF:

0.0446

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0589

Gnomad OTH

AF:

0.0499

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

GnomAD4 genome

AF:

0.0524

AC:

7976

AN:

152266

Hom.:

366

Cov.:

AF XY:

0.0533

AC XY:

3972

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0121

Gnomad4 AMR

AF:

0.0565

Gnomad4 ASJ

AF:

0.0444

Gnomad4 EAS

AF:

0.262

Gnomad4 SAS

AF:

0.0895

Gnomad4 FIN

AF:

0.0446

Gnomad4 NFE

AF:

0.0589

Gnomad4 OTH

AF:

0.0536

Alfa

AF:

0.0643

Hom.:

714

Bravo

AF:

0.0532

Asia WGS

AF:

0.146

AC:

507

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.9

DANN

Benign

0.66

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