17-50072022-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_002204.4(ITGA3):​c.996C>T​(p.Phe332=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,613,448 control chromosomes in the GnomAD database, including 16,649 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3528 hom., cov: 31)
Exomes 𝑓: 0.11 ( 13121 hom. )

Consequence

ITGA3
NM_002204.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.999
Variant links:
Genes affected
ITGA3 (HGNC:6139): (integrin subunit alpha 3) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function as cell surface adhesion molecules. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 3 subunit. This subunit joins with a beta 1 subunit to form an integrin that interacts with extracellular matrix proteins including members of the laminin family. Expression of this gene may be correlated with breast cancer metastasis. [provided by RefSeq, Oct 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 17-50072022-C-T is Benign according to our data. Variant chr17-50072022-C-T is described in ClinVar as [Benign]. Clinvar id is 1271410.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.999 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITGA3NM_002204.4 linkuse as main transcriptc.996C>T p.Phe332= synonymous_variant 7/26 ENST00000320031.13 NP_002195.1
ITGA3XM_047435922.1 linkuse as main transcriptc.996C>T p.Phe332= synonymous_variant 7/18 XP_047291878.1
ITGA3XM_005257308.3 linkuse as main transcriptc.751+1092C>T intron_variant XP_005257365.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITGA3ENST00000320031.13 linkuse as main transcriptc.996C>T p.Phe332= synonymous_variant 7/261 NM_002204.4 ENSP00000315190 P1P26006-2

Frequencies

GnomAD3 genomes
AF:
0.185
AC:
28077
AN:
151844
Hom.:
3511
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.336
Gnomad AMI
AF:
0.0813
Gnomad AMR
AF:
0.224
Gnomad ASJ
AF:
0.118
Gnomad EAS
AF:
0.315
Gnomad SAS
AF:
0.255
Gnomad FIN
AF:
0.0975
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.0889
Gnomad OTH
AF:
0.165
GnomAD3 exomes
AF:
0.167
AC:
41908
AN:
250798
Hom.:
4639
AF XY:
0.162
AC XY:
21919
AN XY:
135622
show subpopulations
Gnomad AFR exome
AF:
0.344
Gnomad AMR exome
AF:
0.250
Gnomad ASJ exome
AF:
0.113
Gnomad EAS exome
AF:
0.320
Gnomad SAS exome
AF:
0.234
Gnomad FIN exome
AF:
0.0991
Gnomad NFE exome
AF:
0.0927
Gnomad OTH exome
AF:
0.141
GnomAD4 exome
AF:
0.114
AC:
166596
AN:
1461486
Hom.:
13121
Cov.:
33
AF XY:
0.116
AC XY:
84575
AN XY:
727078
show subpopulations
Gnomad4 AFR exome
AF:
0.342
Gnomad4 AMR exome
AF:
0.246
Gnomad4 ASJ exome
AF:
0.115
Gnomad4 EAS exome
AF:
0.316
Gnomad4 SAS exome
AF:
0.234
Gnomad4 FIN exome
AF:
0.0970
Gnomad4 NFE exome
AF:
0.0850
Gnomad4 OTH exome
AF:
0.132
GnomAD4 genome
AF:
0.185
AC:
28157
AN:
151962
Hom.:
3528
Cov.:
31
AF XY:
0.189
AC XY:
14048
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.337
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.118
Gnomad4 EAS
AF:
0.316
Gnomad4 SAS
AF:
0.254
Gnomad4 FIN
AF:
0.0975
Gnomad4 NFE
AF:
0.0889
Gnomad4 OTH
AF:
0.169
Alfa
AF:
0.118
Hom.:
1935
Bravo
AF:
0.199
Asia WGS
AF:
0.292
AC:
1016
AN:
3478
EpiCase
AF:
0.0936
EpiControl
AF:
0.0961

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
CADD
Benign
8.8
DANN
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs2269772; hg19: chr17-48149386; COSMIC: COSV50306944; COSMIC: COSV50306944; API