rs1911155

Variant names:

• chr15-84118883-A-G
• rs1911155
• ENST00000558550.2:n.683-2207A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558550.2(ENSG00000291062):​n.683-2207A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,212 control chromosomes in the GnomAD database, including 3,694 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 0.19 (3694 hom., cov: 32)
• Consequence: ENSG00000291062 ENST00000558550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 12 publications found

Genes affected

ENSG00000291062 (HGNC:):

EFL1P1 (HGNC:31739): (elongation factor like GTPase 1 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFL1P1	NR_036652.1	n.709-2207A>G		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291062	ENST00000558550.2	n.683-2207A>G		intron_variant	Intron 6 of 9	3
ENSG00000291062	ENST00000560381.2	n.249-2207A>G		intron_variant	Intron 3 of 8	3
EFL1P1	ENST00000560401.5	n.1337-2207A>G		intron_variant	Intron 11 of 13	6

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29528 AN: 152094 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.194 AC: 29523 AN: 152212 Hom.: 3694 Cov.: 32 AF XY: 0.193 AC XY: 14378 AN XY: 74398

African (AFR) AF: 0.0460 AC: 1911 AN: 41566

American (AMR) AF: 0.199 AC: 3037 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3468

East Asian (EAS) AF: 0.0505 AC: 262 AN: 5186

South Asian (SAS) AF: 0.225 AC: 1086 AN: 4822

European-Finnish (FIN) AF: 0.260 AC: 2749 AN: 10576

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18531 AN: 67988

Other (OTH) AF: 0.210 AC: 443 AN: 2110

Alfa AF: 0.249 Hom.: 16287

Bravo AF: 0.184

Asia WGS AF: 0.143 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1911155; hg19: chr15-84787635;