ENST00000456616.2:n.397-3575C>T

Variant names:

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

Variant summary

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

The ENST00000456616.2(ELOVL2-AS1):​n.397-3575C>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
• Publications: 19 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456616.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2-AS1	NR_038962.1		n.368-3575C>T		intron	N/A
	ELOVL2-AS1	NR_038963.1		n.160-3575C>T		intron	N/A
	ELOVL2-AS1	NR_038964.1		n.361+569C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2-AS1	ENST00000456616.2	TSL:1	n.397-3575C>T		intron	N/A
	ELOVL2-AS1	ENST00000456190.6	TSL:3	n.359+569C>T		intron	N/A
	ELOVL2-AS1	ENST00000606532.6	TSL:4	n.329-3575C>T		intron	N/A

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

African (AFR) AF: 0.792 AC: 32782 AN: 41386

American (AMR) AF: 0.662 AC: 10081 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4654 AN: 5142

South Asian (SAS) AF: 0.664 AC: 3199 AN: 4818

European-Finnish (FIN) AF: 0.482 AC: 4981 AN: 10332

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29591 AN: 67912

Other (OTH) AF: 0.583 AC: 1229 AN: 2108

Alfa AF: 0.489 Hom.: 55068

Bravo AF: 0.610

Asia WGS AF: 0.760 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.24
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs4711171; hg19: chr6-11074347;