rs12662634

Variant names:

• chr6-11073958-G-A
• rs12662634
• ENST00000456616.2:n.397-3731G>A

Variant summary

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

The ENST00000456616.2(ELOVL2-AS1):​n.397-3731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,002 control chromosomes in the GnomAD database, including 3,273 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 0.18 (3273 hom., cov: 32)
• Consequence: ELOVL2-AS1 ENST00000456616.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 5 publications found

Genes affected

ELOVL2-AS1 (HGNC:44156): (ELOVL2 antisense RNA 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 (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2-AS1	NR_038962.1	n.368-3731G>A		intron_variant	Intron 2 of 2
ELOVL2-AS1	NR_038963.1	n.160-3731G>A		intron_variant	Intron 2 of 2
ELOVL2-AS1	NR_038964.1	n.361+413G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL2-AS1	ENST00000456616.2	n.397-3731G>A		intron_variant	Intron 2 of 2	1
ELOVL2-AS1	ENST00000456190.6	n.359+413G>A		intron_variant	Intron 4 of 4	3
ELOVL2-AS1	ENST00000606532.6	n.329-3731G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27103 AN: 151884 Hom.: 3272 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.178 AC: 27107 AN: 152002 Hom.: 3273 Cov.: 32 AF XY: 0.189 AC XY: 14047 AN XY: 74296

African (AFR) AF: 0.0449 AC: 1863 AN: 41490

American (AMR) AF: 0.270 AC: 4127 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3464

East Asian (EAS) AF: 0.448 AC: 2310 AN: 5162

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4812

European-Finnish (FIN) AF: 0.317 AC: 3331 AN: 10516

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12636 AN: 67984

Other (OTH) AF: 0.158 AC: 334 AN: 2110

Alfa AF: 0.189 Hom.: 1540

Bravo AF: 0.167

Asia WGS AF: 0.348 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.77
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs12662634; hg19: chr6-11074191;