12-12330282-C-T

Variant names:

• chr12-12330282-C-T
• rs1192261547
• NM_018050.4:c.1041G>A

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

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

ACMG classification

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
MANSC1	NM_018050.4	c.1041G>A	p.Glu347Glu	synonymous_variant	Exon 4 of 4	ENST00000535902.6	NP_060520.2
MANSC1	NM_001363613.2	c.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
MANSC1	ENST00000535902.6	c.1041G>A	p.Glu347Glu	synonymous_variant	Exon 4 of 4	1	NM_018050.4	ENSP00000438205.1
MANSC1	ENST00000396349.3	c.939G>A	p.Glu313Glu	synonymous_variant	Exon 5 of 5	2		ENSP00000379638.3
MANSC1	ENST00000545735.1	c.798G>A	p.Glu266Glu	synonymous_variant	Exon 2 of 2	2		ENSP00000445303.1

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

Other links and lift over

dbSNP: rs1192261547; hg19: chr12-12483216;