15-82210737-T-C

Position:

• chr15-82210737-T-C

Variant summary

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

The NM_024580.6(EFL1):​c.1750+3980A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,650 control chromosomes in the GnomAD database, including 7,828 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 0.31 (7828 hom., cov: 30)
• Consequence: EFL1 NM_024580.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

EFL1 (HGNC:25789): (elongation factor like GTPase 1) Enables GTPase activity and ribosome binding activity. Involved in GTP metabolic process and mature ribosome assembly. Predicted to be part of ribonucleoprotein complex. Implicated in Shwachman-Diamond syndrome. [provided by Alliance of Genome Resources, Apr 2022]

EFL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFL1	NM_024580.6	c.1750+3980A>G		intron_variant		ENST00000268206.12	NP_078856.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFL1	ENST00000268206.12	c.1750+3980A>G		intron_variant		1	NM_024580.6	ENSP00000268206.7

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47575 AN: 151532 Hom.: 7820 Cov.: 30

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.314 AC: 47619 AN: 151650 Hom.: 7828 Cov.: 30 AF XY: 0.305 AC XY: 22612 AN XY: 74070

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.311

Alfa AF: 0.329 Hom.: 1020

Bravo AF: 0.317

Asia WGS AF: 0.195 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.49

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: rs4778983; hg19: chr15-82503078;