15-68422693-A-G

Variant names:

• chr15-68422693-A-G
• rs7164335
• NM_001004439.2:c.52+9322T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004439.2(ITGA11):​c.52+9322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,980 control chromosomes in the GnomAD database, including 40,361 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 0.72 (40361 hom., cov: 31)
• Consequence: ITGA11 NM_001004439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 12 publications found

Genes affected

ITGA11 (HGNC:6136): (integrin subunit alpha 11) This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein contains an I domain, is expressed in muscle tissue, dimerizes with beta 1 integrin in vitro, and appears to bind collagen in this form. Therefore, the protein may be involved in attaching muscle tissue to the extracellular matrix. Alternative transcriptional splice variants have been found for this gene, but their biological validity is not determined. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA11	NM_001004439.2	c.52+9322T>C		intron_variant	Intron 1 of 29	ENST00000315757.9	NP_001004439.1
ITGA11	XM_011521363.3	c.52+9322T>C		intron_variant	Intron 1 of 27		XP_011519665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA11	ENST00000315757.9	c.52+9322T>C		intron_variant	Intron 1 of 29	1	NM_001004439.2	ENSP00000327290.7
ITGA11	ENST00000423218.6	c.52+9322T>C		intron_variant	Intron 1 of 29	2		ENSP00000403392.2

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109081 AN: 151862 Hom.: 40306 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.719 AC: 109201 AN: 151980 Hom.: 40361 Cov.: 31 AF XY: 0.707 AC XY: 52528 AN XY: 74254

African (AFR) AF: 0.901 AC: 37369 AN: 41490

American (AMR) AF: 0.669 AC: 10238 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2497 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3255 AN: 5122

South Asian (SAS) AF: 0.544 AC: 2613 AN: 4802

European-Finnish (FIN) AF: 0.529 AC: 5569 AN: 10536

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.666 AC: 45231 AN: 67958

Other (OTH) AF: 0.728 AC: 1536 AN: 2110

Alfa AF: 0.695 Hom.: 31824

Bravo AF: 0.741

Asia WGS AF: 0.648 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.39
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7164335; hg19: chr15-68715032;