12-12330282-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_018050.4(MANSC1):​c.1041G>A​(p.Glu347Glu) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

MANSC1
NM_018050.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0800
Variant links:
Genes affected
MANSC1 (HGNC:25505): (MANSC domain containing 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP7
Synonymous conserved (PhyloP=-0.08 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MANSC1NM_018050.4 linkc.1041G>A p.Glu347Glu synonymous_variant Exon 4 of 4 ENST00000535902.6 NP_060520.2 Q9H8J5-1
MANSC1NM_001363613.2 linkc.939G>A p.Glu313Glu synonymous_variant Exon 5 of 5 NP_001350542.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MANSC1ENST00000535902.6 linkc.1041G>A p.Glu347Glu synonymous_variant Exon 4 of 4 1 NM_018050.4 ENSP00000438205.1 Q9H8J5-1
MANSC1ENST00000396349.3 linkc.939G>A p.Glu313Glu synonymous_variant Exon 5 of 5 2 ENSP00000379638.3 Q9H8J5-2
MANSC1ENST00000545735.1 linkc.798G>A p.Glu266Glu synonymous_variant Exon 2 of 2 2 ENSP00000445303.1 F5H3M3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
0.28
DANN
Benign
0.35

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: rs1192261547; hg19: chr12-12483216; API