NM_001004439.2:c.52+6354G>A

Variant names:

• chr15-68425661-C-T
• rs16952059
• NM_001004439.2:c.52+6354G>A

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+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
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004439.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA11	NM_001004439.2	MANE Select	c.52+6354G>A		intron	N/A	NP_001004439.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA11	ENST00000315757.9	TSL:1 MANE Select	c.52+6354G>A		intron	N/A	ENSP00000327290.7
	ITGA11	ENST00000423218.6	TSL:2	c.52+6354G>A		intron	N/A	ENSP00000403392.2

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

African (AFR) AF: 0.283 AC: 11739 AN: 41516

American (AMR) AF: 0.0986 AC: 1508 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5176

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1505 AN: 10602

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0611 AC: 4154 AN: 68032

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0786 Hom.: 1234

Bravo AF: 0.133

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.67
PhyloP100		-0.10
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: rs16952059; hg19: chr15-68718000;