rs10512997

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000282588.7(ITGA1):​c.61+20515C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,358 control chromosomes in the GnomAD database, including 5,578 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 0.27 ( 5578 hom., cov: 30)

Consequence

ITGA1
ENST00000282588.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0800
Variant links:
Genes affected
ITGA1 (HGNC:6134): (integrin subunit alpha 1) This gene encodes the alpha 1 subunit of integrin receptors. This protein heterodimerizes with the beta 1 subunit to form a cell-surface receptor for collagen and laminin. The heterodimeric receptor is involved in cell-cell adhesion and may play a role in inflammation and fibrosis. The alpha 1 subunit contains an inserted (I) von Willebrand factor type I domain which is thought to be involved in collagen binding. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITGA1NM_181501.2 linkuse as main transcriptc.61+20515C>T intron_variant ENST00000282588.7 NP_852478.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITGA1ENST00000282588.7 linkuse as main transcriptc.61+20515C>T intron_variant 1 NM_181501.2 ENSP00000282588 P1
ITGA1ENST00000650673.1 linkuse as main transcriptc.61+20515C>T intron_variant, NMD_transcript_variant ENSP00000498529
ITGA1ENST00000504086.1 linkuse as main transcriptn.469-15384C>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.265
AC:
40077
AN:
151240
Hom.:
5567
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.214
Gnomad ASJ
AF:
0.336
Gnomad EAS
AF:
0.185
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.319
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.305
Gnomad OTH
AF:
0.266
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.265
AC:
40116
AN:
151358
Hom.:
5578
Cov.:
30
AF XY:
0.262
AC XY:
19385
AN XY:
73968
show subpopulations
Gnomad4 AFR
AF:
0.220
Gnomad4 AMR
AF:
0.215
Gnomad4 ASJ
AF:
0.336
Gnomad4 EAS
AF:
0.185
Gnomad4 SAS
AF:
0.185
Gnomad4 FIN
AF:
0.319
Gnomad4 NFE
AF:
0.305
Gnomad4 OTH
AF:
0.266
Alfa
AF:
0.289
Hom.:
3015
Bravo
AF:
0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
3.0
DANN
Benign
0.57

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10512997; hg19: chr5-52104763; API