6-159907710-A-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_002377.4(MAS1):āc.755A>Gā(p.Tyr252Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00234 in 1,613,268 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0020 ( 1 hom., cov: 30)
Exomes š: 0.0024 ( 6 hom. )
Consequence
MAS1
NM_002377.4 missense
NM_002377.4 missense
Scores
9
10
Clinical Significance
Conservation
PhyloP100: 2.07
Genes affected
MAS1 (HGNC:6899): (MAS1 proto-oncogene, G protein-coupled receptor) This gene encodes a class I seven-transmembrane G-protein-coupled receptor. The encoded protein is a receptor for angiotensin-(1-7) and preferentially couples to the Gq protein, activating the phospholipase C signaling pathway. The encoded protein may play a role in multiple processes including hypotension, smooth muscle relaxation and cardioprotection by mediating the effects of angiotensin-(1-7). [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 6-159907710-A-G is Benign according to our data. Variant chr6-159907710-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 719390.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAS1 | NM_002377.4 | c.755A>G | p.Tyr252Cys | missense_variant | 3/3 | ENST00000674077.2 | |
MAS1 | NM_001366704.2 | c.755A>G | p.Tyr252Cys | missense_variant | 2/2 | ||
MAS1 | XM_047418776.1 | c.755A>G | p.Tyr252Cys | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAS1 | ENST00000674077.2 | c.755A>G | p.Tyr252Cys | missense_variant | 3/3 | NM_002377.4 | P1 | ||
MAS1 | ENST00000252660.5 | c.755A>G | p.Tyr252Cys | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00201 AC: 305AN: 151432Hom.: 1 Cov.: 30
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GnomAD3 exomes AF: 0.00242 AC: 608AN: 251392Hom.: 1 AF XY: 0.00244 AC XY: 332AN XY: 135862
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GnomAD4 exome AF: 0.00238 AC: 3472AN: 1461718Hom.: 6 Cov.: 32 AF XY: 0.00239 AC XY: 1739AN XY: 727166
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GnomAD4 genome AF: 0.00200 AC: 303AN: 151550Hom.: 1 Cov.: 30 AF XY: 0.00200 AC XY: 148AN XY: 74026
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at