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GeneBe

5-52861513-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_181501.2(ITGA1):c.249A>G(p.Pro83=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00514 in 1,613,816 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0053 ( 22 hom. )

Consequence

ITGA1
NM_181501.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0650
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 -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-52861513-A-G is Benign according to our data. Variant chr5-52861513-A-G is described in ClinVar as [Benign]. Clinvar id is 713618.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.065 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ITGA1NM_181501.2 linkuse as main transcriptc.249A>G p.Pro83= synonymous_variant 3/29 ENST00000282588.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ITGA1ENST00000282588.7 linkuse as main transcriptc.249A>G p.Pro83= synonymous_variant 3/291 NM_181501.2 P1
ENST00000652796.1 linkuse as main transcriptn.504-6535T>C intron_variant, non_coding_transcript_variant
ITGA1ENST00000650673.1 linkuse as main transcriptc.249A>G p.Pro83= synonymous_variant, NMD_transcript_variant 3/29

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00378
AC:
575
AN:
152166
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00116
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00707
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.000943
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00573
Gnomad OTH
AF:
0.00382
GnomAD3 exomes
AF:
0.00378
AC:
951
AN:
251336
Hom.:
3
AF XY:
0.00367
AC XY:
498
AN XY:
135850
show subpopulations
Gnomad AFR exome
AF:
0.000615
Gnomad AMR exome
AF:
0.00527
Gnomad ASJ exome
AF:
0.00169
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000523
Gnomad FIN exome
AF:
0.000693
Gnomad NFE exome
AF:
0.00597
Gnomad OTH exome
AF:
0.00522
GnomAD4 exome
AF:
0.00528
AC:
7718
AN:
1461532
Hom.:
22
Cov.:
30
AF XY:
0.00511
AC XY:
3719
AN XY:
727116
show subpopulations
Gnomad4 AFR exome
AF:
0.00120
Gnomad4 AMR exome
AF:
0.00546
Gnomad4 ASJ exome
AF:
0.00161
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000591
Gnomad4 FIN exome
AF:
0.00101
Gnomad4 NFE exome
AF:
0.00629
Gnomad4 OTH exome
AF:
0.00457
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00378
AC:
575
AN:
152284
Hom.:
2
Cov.:
33
AF XY:
0.00355
AC XY:
264
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.00115
Gnomad4 AMR
AF:
0.00706
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.000943
Gnomad4 NFE
AF:
0.00573
Gnomad4 OTH
AF:
0.00378
Alfa
AF:
0.00471
Hom.:
0
Bravo
AF:
0.00407
Asia WGS
AF:
0.00144
AC:
5
AN:
3478
EpiCase
AF:
0.00764
EpiControl
AF:
0.00712

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
6.9
Dann
Benign
0.76

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: rs61757093; hg19: chr5-52157347; API