ENST00000558550.2:n.683-5280A>G

Variant names:

• chr15-84115810-A-G
• rs6603020
• ENST00000558550.2:n.683-5280A>G

Variant summary

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

The ENST00000558550.2(ENSG00000291062):​n.683-5280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,146 control chromosomes in the GnomAD database, including 5,092 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 0.25 (5092 hom., cov: 33)
• Consequence: ENSG00000291062 ENST00000558550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFL1P1	NR_036652.1	n.609-235A>G		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291062	ENST00000558550.2	n.683-5280A>G		intron_variant	Intron 6 of 9	3
ENSG00000291062	ENST00000560381.2	n.149-235A>G		intron_variant	Intron 2 of 8	3
EFL1P1	ENST00000560401.5	n.1237-235A>G		intron_variant	Intron 10 of 13	6

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38025 AN: 152028 Hom.: 5090 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.250 AC: 38044 AN: 152146 Hom.: 5092 Cov.: 33 AF XY: 0.251 AC XY: 18652 AN XY: 74384

African (AFR) AF: 0.187 AC: 7763 AN: 41518

American (AMR) AF: 0.378 AC: 5772 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1731 AN: 5168

South Asian (SAS) AF: 0.170 AC: 822 AN: 4826

European-Finnish (FIN) AF: 0.236 AC: 2494 AN: 10576

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17856 AN: 67994

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.269 Hom.: 1317

Bravo AF: 0.260

Asia WGS AF: 0.226 AC: 783 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.032
DANN	Benign	0.35
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs6603020; hg19: chr15-84784562;