rs1655231177

Variant names:

• chr1-145895337-C-A
• rs1655231177
• NM_003637.5:c.3171G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-145895337-C-A
• chr1-145895337-C-T

Variant summary

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

The NM_003637.5(ITGA10):​c.3171G>T​(p.Lys1057Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ITGA10 NM_003637.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.15
• Publications: 0 publications found

Genes affected

ITGA10 (HGNC:6135): (integrin subunit alpha 10) Integrins are integral transmembrane glycoproteins composed of noncovalently linked alpha and beta chains. They participate in cell adhesion as well as cell-surface mediated signalling. This gene encodes an integrin alpha chain and is expressed at high levels in chondrocytes, where it is transcriptionally regulated by AP-2epsilon and Ets-1. The protein encoded by this gene binds to collagen. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

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 (MetaRNN=0.124518365).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003637.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA10	NM_003637.5	MANE Select	c.3171G>T	p.Lys1057Asn	missense	Exon 27 of 30	NP_003628.2
	ITGA10	NM_001303040.2		c.2778G>T	p.Lys926Asn	missense	Exon 24 of 27	NP_001289969.1
	ITGA10	NM_001303041.2		c.2742G>T	p.Lys914Asn	missense	Exon 23 of 26	NP_001289970.1	O75578-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA10	ENST00000369304.8	TSL:1 MANE Select	c.3171G>T	p.Lys1057Asn	missense	Exon 27 of 30	ENSP00000358310.3	O75578-1
	ITGA10	ENST00000539363.2	TSL:1	c.2742G>T	p.Lys914Asn	missense	Exon 23 of 26	ENSP00000439894.1	O75578-3
	ITGA10	ENST00000889441.1		c.3078G>T	p.Lys1026Asn	missense	Exon 26 of 29	ENSP00000559500.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_noAF	Benign	-0.45
CADD	Benign	19
DANN	Benign	0.63
DEOGEN2	Benign	0.083	T
LIST_S2	Benign	0.84	T
MetaRNN	Benign	0.12	T
PhyloP100		1.1
PROVEAN	Benign	-0.33	N
Sift	Benign	0.92	T
Sift4G	Benign	0.49	T
Vest4		0.24
gMVP		0.93

Splicing

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

Other links and lift over

dbSNP: rs1655231177; hg19: chr1-145539739;