chr15-68422693-A-G

Position:

• chr15-68422693-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ITGA11	NM_001004439.2	c.52+9322T>C		intron_variant		ENST00000315757.9	NP_001004439.1
ITGA11	XM_011521363.3	c.52+9322T>C		intron_variant			XP_011519665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA11	ENST00000315757.9	c.52+9322T>C		intron_variant		1	NM_001004439.2	ENSP00000327290.7
ITGA11	ENST00000423218.6	c.52+9322T>C		intron_variant		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

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.728

Alfa AF: 0.677 Hom.: 20576

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

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

Other links and lift over

dbSNP: rs7164335; hg19: chr15-68715032;