6-11074114-C-T

Variant names:

• chr6-11074114-C-T
• rs4711171
• ENST00000456616.2:n.397-3575C>T

Variant summary

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

The ENST00000456616.2(ELOVL2-AS1):​n.397-3575C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,594 control chromosomes in the GnomAD database, including 28,288 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 0.59 (28288 hom., cov: 31)
• Consequence: ELOVL2-AS1 ENST00000456616.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2-AS1	NR_038962.1	n.368-3575C>T		intron_variant	Intron 2 of 2
ELOVL2-AS1	NR_038963.1	n.160-3575C>T		intron_variant	Intron 2 of 2
ELOVL2-AS1	NR_038964.1	n.361+569C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL2-AS1	ENST00000456616.2	n.397-3575C>T		intron_variant	Intron 2 of 2	1
ELOVL2-AS1	ENST00000456190.6	n.359+569C>T		intron_variant	Intron 4 of 4	3
ELOVL2-AS1	ENST00000606532.5	n.329-3575C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.587 AC: 88951 AN: 151476 Hom.: 28218 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.588 AC: 89082 AN: 151594 Hom.: 28288 Cov.: 31 AF XY: 0.594 AC XY: 43923 AN XY: 73990

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.583

Alfa AF: 0.474 Hom.: 18070

Bravo AF: 0.610

Asia WGS AF: 0.760 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4711171; hg19: chr6-11074347;