chr3-128319530-C-A

Position:

• chr3-128319530-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_021937.5(EEFSEC):​c.787-21703C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,060 control chromosomes in the GnomAD database, including 16,404 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 0.43 (16404 hom., cov: 33)
• Consequence: EEFSEC NM_021937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.09

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EEFSEC	NM_021937.5	c.787-21703C>A		intron_variant		ENST00000254730.11	NP_068756.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEFSEC	ENST00000254730.11	c.787-21703C>A		intron_variant		1	NM_021937.5	ENSP00000254730	P1
EEFSEC	ENST00000483457.1	c.622-21703C>A		intron_variant		5		ENSP00000417660
EEFSEC	ENST00000484438.1	n.365-21703C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64650 AN: 151942 Hom.: 16380 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.426 AC: 64720 AN: 152060 Hom.: 16404 Cov.: 33 AF XY: 0.427 AC XY: 31731 AN XY: 74332

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.382

Alfa AF: 0.302 Hom.: 14321

Bravo AF: 0.441

Asia WGS AF: 0.451 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	16
DANN	Benign	0.84

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: rs10934853; hg19: chr3-128038373; COSMIC: COSV54620576;