rs12662634

chr6-11073958-G-A

Variant summary

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

The NR_038964.1(ELOVL2-AS1):n.361+413G>A variant causes a intron, non coding transcript 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 NR_038964.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

ELOVL2-AS1 (HGNC:44156): (ELOVL2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ELOVL2-AS1	NR_038964.1	n.361+413G>A		intron_variant, non_coding_transcript_variant
ELOVL2-AS1	NR_038962.1	n.368-3731G>A		intron_variant, non_coding_transcript_variant
ELOVL2-AS1	NR_038963.1	n.160-3731G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL2-AS1	ENST00000661751.1	n.436-3731G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.158

Alfa AF: 0.190 Hom.: 1413

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12662634; hg19: chr6-11074191;