6-11060050-A-T

Variant names:

• chr6-11060050-A-T
• rs9368564
• ENST00000456616.2:n.396+12051A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000456616.2(ELOVL2-AS1):​n.396+12051A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ELOVL2-AS1 ENST00000456616.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL2-AS1	NR_038962.1	n.367+12051A>T		intron_variant	Intron 2 of 2
ELOVL2-AS1	NR_038963.1	n.159+12051A>T		intron_variant	Intron 2 of 2
ELOVL2-AS1	NR_038964.1	n.270+10831A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL2-AS1	ENST00000456616.2	n.396+12051A>T		intron_variant	Intron 2 of 2	1
ELOVL2-AS1	ENST00000456190.6	n.268+10831A>T		intron_variant	Intron 3 of 4	3
ELOVL2-AS1	ENST00000606532.6	n.328+12051A>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 517

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.71
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs9368564; hg19: chr6-11060283;