15-29268896-G-T

Variant names:

• chr15-29268896-G-T
• NM_138704.4:c.810C>A
• NSMCE3 p.Val270Val

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_138704.4(NSMCE3):​c.810C>A​(p.Val270Val) 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. Synonymous variant affecting the same amino acid position (i.e. V270V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NSMCE3 NM_138704.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 0 publications found

Genes affected

NSMCE3 (HGNC:7677): (NSE3 homolog, SMC5-SMC6 complex component) The protein encoded by this gene is part of the SMC5-6 chromatin reorganizing complex and is a member of the MAGE superfamily. This is an intronless gene. [provided by RefSeq, May 2011]

ENTREP2 (HGNC:29075): (endosomal transmembrane epsin interactor 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP7: Synonymous conserved (PhyloP=-0.304 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138704.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSMCE3	NM_138704.4	MANE Select	c.810C>A	p.Val270Val	synonymous	Exon 1 of 1	NP_619649.1	Q96MG7
	ENTREP2	NM_015307.2	MANE Select	c.277-16418C>A		intron	N/A	NP_056122.1	O60320-1
	ENTREP2	NM_001387214.1		c.277-16418C>A		intron	N/A	NP_001374143.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSMCE3	ENST00000332303.6	TSL:6 MANE Select	c.810C>A	p.Val270Val	synonymous	Exon 1 of 1	ENSP00000330694.4	Q96MG7
	ENTREP2	ENST00000261275.5	TSL:5 MANE Select	c.277-16418C>A		intron	N/A	ENSP00000261275.4	O60320-1
	ENTREP2	ENST00000918355.1		c.277-16418C>A		intron	N/A	ENSP00000588414.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.2
DANN	Benign	0.87
PhyloP100		-0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr15-29561100;