rs2811392

chr3-128305133-G-Achr3-128305133-G-Cchr3-128305133-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021937.5(EEFSEC):c.787-36100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,076 control chromosomes in the GnomAD database, including 56,045 homozygotes. 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: 𝑓 0.86 (56045 hom., cov: 33)
• Consequence: EEFSEC NM_021937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

Genes affected

EEFSEC (HGNC:24614): (eukaryotic elongation factor, selenocysteine-tRNA specific) Predicted to enable translation elongation factor activity. Predicted to be involved in selenocysteine incorporation. Predicted to be located in cytoplasm and nucleus. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEFSEC	NM_021937.5	c.787-36100G>A		intron_variant		ENST00000254730.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEFSEC	ENST00000254730.11	c.787-36100G>A		intron_variant		1	NM_021937.5	P1
EEFSEC	ENST00000483457.1	c.622-36100G>A		intron_variant		5
EEFSEC	ENST00000484438.1	n.365-36100G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130169 AN: 151958 Hom.: 55988 Cov.: 33

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.868

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.857 AC: 130285 AN: 152076 Hom.: 56045 Cov.: 33 AF XY: 0.858 AC XY: 63816 AN XY: 74348

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.869

Alfa AF: 0.862 Hom.: 7042

Bravo AF: 0.856

Asia WGS AF: 0.916 AC: 3177 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.8
Dann	Benign	0.56

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: rs2811392; hg19: chr3-128023976; COSMIC: COSV54623179;