rs776709976
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_002206.3(ITGA7):c.1071G>A(p.Val357Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000178 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
ITGA7
NM_002206.3 synonymous
NM_002206.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.34
Publications
1 publications found
Genes affected
ITGA7 (HGNC:6143): (integrin subunit alpha 7) The protein encoded by this gene belongs to the integrin alpha chain family. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. They mediate a wide spectrum of cell-cell and cell-matrix interactions, and thus play a role in cell migration, morphologic development, differentiation, and metastasis. This protein functions as a receptor for the basement membrane protein laminin-1. It is mainly expressed in skeletal and cardiac muscles and may be involved in differentiation and migration processes during myogenesis. Defects in this gene are associated with congenital myopathy. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Feb 2009]
ITGA7 Gene-Disease associations (from GenCC):
- congenital muscular dystrophy due to integrin alpha-7 deficiencyInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
- congenital fiber-type disproportion myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP6
Variant 12-55698504-C-T is Benign according to our data. Variant chr12-55698504-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 538010.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002206.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ITGA7 | NM_002206.3 | MANE Select | c.1071G>A | p.Val357Val | synonymous | Exon 7 of 25 | NP_002197.2 | ||
| ITGA7 | NM_001410977.1 | c.1203G>A | p.Val401Val | synonymous | Exon 8 of 26 | NP_001397906.1 | |||
| ITGA7 | NM_001144996.2 | c.1083G>A | p.Val361Val | synonymous | Exon 7 of 25 | NP_001138468.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ITGA7 | ENST00000257879.11 | TSL:1 MANE Select | c.1071G>A | p.Val357Val | synonymous | Exon 7 of 25 | ENSP00000257879.7 | ||
| ITGA7 | ENST00000553804.6 | TSL:1 | c.1083G>A | p.Val361Val | synonymous | Exon 7 of 25 | ENSP00000452120.1 | ||
| ITGA7 | ENST00000555728.5 | TSL:5 | c.1203G>A | p.Val401Val | synonymous | Exon 8 of 26 | ENSP00000452387.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251458 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
5
AN:
251458
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461878Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727246 show subpopulations
GnomAD4 exome
AF:
AC:
26
AN:
1461878
Hom.:
Cov.:
33
AF XY:
AC XY:
11
AN XY:
727246
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
2
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
24
AN:
1112004
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
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Bravo
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EpiCase
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ClinVar
ClinVar submissions as Germline
Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Congenital muscular dystrophy due to integrin alpha-7 deficiency (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 7
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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