rs1386417351

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_052967.2(MAS1L):​c.616A>T​(p.Ile206Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

MAS1L
NM_052967.2 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100
Variant links:
Genes affected
MAS1L (HGNC:13961): (MAS1 proto-oncogene like, G protein-coupled receptor) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08550057).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAS1LNM_052967.2 linkc.616A>T p.Ile206Leu missense_variant Exon 1 of 1 ENST00000377127.4 NP_443199.1 P35410W8W3J1Q502V9
LOC105375008XR_007059916.1 linkn.394+2124T>A intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAS1LENST00000377127.4 linkc.616A>T p.Ile206Leu missense_variant Exon 1 of 1 6 NM_052967.2 ENSP00000366331.3 P35410
ENSG00000289203ENST00000688607.1 linkn.1583+220A>T intron_variant Intron 6 of 6

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
3.7
DANN
Benign
0.74
DEOGEN2
Benign
0.015
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.0021
N
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.086
T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
0.40
N
PrimateAI
Benign
0.38
T
PROVEAN
Benign
-0.52
N
REVEL
Benign
0.044
Sift
Benign
0.30
T
Sift4G
Benign
0.42
T
Polyphen
0.041
B
Vest4
0.16
MutPred
0.45
Loss of methylation at K208 (P = 0.0554);
MVP
0.23
MPC
0.071
ClinPred
0.12
T
GERP RS
-0.79
Varity_R
0.050
gMVP
0.059

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: rs1386417351; hg19: chr6-29455064; API