chr15-68343437-A-G

Variant names:

• chr15-68343437-A-G
• rs1563894
• NM_001004439.2:c.1132-3793T>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.1132-3793T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,182 control chromosomes in the GnomAD database, including 3,950 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 0.22 (3950 hom., cov: 32)
• Consequence: ITGA11 NM_001004439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 8 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA11	NM_001004439.2	c.1132-3793T>C		intron_variant	Intron 10 of 29	ENST00000315757.9	NP_001004439.1
ITGA11	XM_011521363.3	c.925-3793T>C		intron_variant	Intron 8 of 27		XP_011519665.1
ITGA11	XM_005254228.4	c.826-3793T>C		intron_variant	Intron 8 of 27		XP_005254285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA11	ENST00000315757.9	c.1132-3793T>C		intron_variant	Intron 10 of 29	1	NM_001004439.2	ENSP00000327290.7
ITGA11	ENST00000423218.6	c.1132-3793T>C		intron_variant	Intron 10 of 29	2		ENSP00000403392.2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33735 AN: 152064 Hom.: 3948 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.222 AC: 33775 AN: 152182 Hom.: 3950 Cov.: 32 AF XY: 0.220 AC XY: 16343 AN XY: 74420

African (AFR) AF: 0.270 AC: 11220 AN: 41498

American (AMR) AF: 0.168 AC: 2578 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3472

East Asian (EAS) AF: 0.130 AC: 676 AN: 5186

South Asian (SAS) AF: 0.132 AC: 638 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2593 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14751 AN: 67990

Other (OTH) AF: 0.223 AC: 471 AN: 2112

Alfa AF: 0.211 Hom.: 8958

Bravo AF: 0.218

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.6
DANN	Benign	0.76
PhyloP100		0.96
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: rs1563894; hg19: chr15-68635775;