3-47504364-C-A

Variant names:

• chr3-47504364-C-A
• rs751435514
• NM_001031703.3:c.289G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001031703.3(ELP6):​c.289G>T​(p.Ala97Ser) 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A97T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ELP6 NM_001031703.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 0 publications found

Genes affected

ELP6 (HGNC:25976): (elongator acetyltransferase complex subunit 6) Predicted to be involved in positive regulation of cell migration. Located in cytosol and nucleus. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.027604371).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELP6	NM_001031703.3	c.289G>T	p.Ala97Ser	missense_variant	Exon 4 of 7	ENST00000296149.9	NP_001026873.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELP6	ENST00000296149.9	c.289G>T	p.Ala97Ser	missense_variant	Exon 4 of 7	1	NM_001031703.3	ENSP00000296149.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.056
DANN	Benign	0.71
DEOGEN2	Benign	0.0066	T;T;T;T;T;T;T;T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.062	N
LIST_S2	Benign	0.56	T;.;T;T;T;T;T;T
M_CAP	Benign	0.0018	T
MetaRNN	Benign	0.028	T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.70	N;.;.;.;.;.;.;.
PhyloP100		-0.93
PrimateAI	Benign	0.27	T
PROVEAN	Benign	0.37	N;N;N;N;N;N;N;N
REVEL	Benign	0.13
Sift	Benign	0.67	T;T;T;T;T;T;T;T
Sift4G	Benign	1.0	T;T;T;.;T;.;T;T
Polyphen		0.0	B;.;.;.;.;.;.;.
Vest4		0.17
MutPred		0.26		Gain of disorder (P = 0.036);.;.;.;.;.;.;.;
MVP		0.28
MPC		0.33
ClinPred		0.026	T
GERP RS		-4.5
Varity_R		0.033
gMVP		0.17
Mutation Taster		=96/4	polymorphism

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

Other links and lift over

dbSNP: rs751435514; hg19: chr3-47545854; COSMIC: COSV56132542; COSMIC: COSV56132542;