rs16952059

chr15-68425661-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004439.2(ITGA11):c.52+6354G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,236 control chromosomes in the GnomAD database, including 2,081 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 0.13 (2081 hom., cov: 32)
• Consequence: ITGA11 NM_001004439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA11	NM_001004439.2	c.52+6354G>A		intron_variant		ENST00000315757.9
ITGA11	XM_011521363.3	c.52+6354G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA11	ENST00000315757.9	c.52+6354G>A		intron_variant		1	NM_001004439.2	P4
ITGA11	ENST00000423218.6	c.52+6354G>A		intron_variant		2		A1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19913 AN: 152118 Hom.: 2075 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.0752

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.131 AC: 19932 AN: 152236 Hom.: 2081 Cov.: 32 AF XY: 0.133 AC XY: 9871 AN XY: 74448

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.0986

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.0998

Alfa AF: 0.0718 Hom.: 778

Bravo AF: 0.133

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.4
Dann	Benign	0.67

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: rs16952059; hg19: chr15-68718000;