rs2811485

Positions:

• chr3-128200203-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.316+46380G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,730 control chromosomes in the GnomAD database, including 16,198 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 0.42 (16198 hom., cov: 33)
• Consequence: EEFSEC NM_021937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEFSEC	NM_021937.5	c.316+46380G>T		intron_variant		ENST00000254730.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEFSEC	ENST00000254730.11	c.316+46380G>T		intron_variant		1	NM_021937.5	P1
EEFSEC	ENST00000483457.1	c.316+46380G>T		intron_variant		5
EEFSEC	ENST00000484438.1	n.156+46380G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64038 AN: 151612 Hom.: 16166 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.423 AC: 64129 AN: 151730 Hom.: 16198 Cov.: 33 AF XY: 0.423 AC XY: 31358 AN XY: 74154

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.380

Alfa AF: 0.320 Hom.: 2124

Bravo AF: 0.441

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.47

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: rs2811485; hg19: chr3-127919046;