rs7178655

Variant names:

• chr15-84095489-T-G
• rs7178655
• ENST00000558187.5:n.412+5196T>G

Variant summary

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

The ENST00000558187.5(ENSG00000291062):​n.412+5196T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,012 control chromosomes in the GnomAD database, including 24,321 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 0.53 (24321 hom., cov: 31)
• Consequence: ENSG00000291062 ENST00000558187.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFL1P1	NR_036652.1	n.393+5196T>G		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291062	ENST00000558187.5	n.412+5196T>G		intron_variant	Intron 4 of 5	4
ENSG00000291062	ENST00000558550.2	n.333+5196T>G		intron_variant	Intron 4 of 9	3
EFL1P1	ENST00000560401.5	n.412+5196T>G		intron_variant	Intron 4 of 13	6

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80284 AN: 151894 Hom.: 24322 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.528 AC: 80296 AN: 152012 Hom.: 24321 Cov.: 31 AF XY: 0.524 AC XY: 38954 AN XY: 74312

African (AFR) AF: 0.247 AC: 10225 AN: 41464

American (AMR) AF: 0.481 AC: 7339 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2317 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1343 AN: 5142

South Asian (SAS) AF: 0.535 AC: 2570 AN: 4808

European-Finnish (FIN) AF: 0.710 AC: 7507 AN: 10576

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.690 AC: 46895 AN: 67970

Other (OTH) AF: 0.591 AC: 1246 AN: 2108

Alfa AF: 0.629 Hom.: 29094

Bravo AF: 0.499

Asia WGS AF: 0.421 AC: 1466 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7178655; hg19: chr15-84764241;