rs9368564

Positions:

• chr6-11060050-A-G
• chr6-11060050-A-T

Variant summary

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

The NR_038964.1(ELOVL2-AS1):​n.270+10831A>G 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 0.18 in 151,906 control chromosomes in the GnomAD database, including 3,125 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 (3125 hom., cov: 32)
• Consequence: ELOVL2-AS1 NR_038964.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL2-AS1	NR_038964.1	n.270+10831A>G		intron_variant, non_coding_transcript_variant
ELOVL2-AS1	NR_038962.1	n.367+12051A>G		intron_variant, non_coding_transcript_variant
ELOVL2-AS1	NR_038963.1	n.159+12051A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL2-AS1	ENST00000661751.1	n.435+12051A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27346 AN: 151806 Hom.: 3120 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.180 AC: 27353 AN: 151906 Hom.: 3125 Cov.: 32 AF XY: 0.178 AC XY: 13197 AN XY: 74260

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.242

Alfa AF: 0.187 Hom.: 412

Bravo AF: 0.183

Asia WGS AF: 0.259 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9368564; hg19: chr6-11060283;