15-68302737-A-G

Variant names:

• chr15-68302737-A-G
• rs56165498
• NM_001004439.2:c.*322T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001004439.2(ITGA11):​c.*322T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000647 in 154,650 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000065 (0 hom.)
• Consequence: ITGA11 NM_001004439.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).

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.*322T>C		3_prime_UTR	Exon 30 of 30	NP_001004439.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA11	ENST00000315757.9	TSL:1 MANE Select	c.*322T>C		3_prime_UTR	Exon 30 of 30	ENSP00000327290.7
	ITGA11	ENST00000423218.6	TSL:2	c.*322T>C		3_prime_UTR	Exon 30 of 30	ENSP00000403392.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000647 AC: 1 AN: 154650 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 78540

African (AFR) AF: 0.00 AC: 0 AN: 4462

American (AMR) AF: 0.00 AC: 0 AN: 3880

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5732

East Asian (EAS) AF: 0.00 AC: 0 AN: 10050

South Asian (SAS) AF: 0.00 AC: 0 AN: 8080

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 836

European-Non Finnish (NFE) AF: 0.00000994 AC: 1 AN: 100592

Other (OTH) AF: 0.00 AC: 0 AN: 10422

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs56165498; hg19: chr15-68595075;