6-11075793-T-G

Variant names:

• chr6-11075793-T-G
• rs1321535
• ENST00000456616.2:n.397-1896T>G

Variant summary

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

The ENST00000456616.2(ELOVL2-AS1):​n.397-1896T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,010 control chromosomes in the GnomAD database, including 14,015 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 0.42 (14015 hom., cov: 32)
• Consequence: ELOVL2-AS1 ENST00000456616.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 15 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 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.368-1896T>G		intron	N/A
	ELOVL2-AS1	NR_038963.1		n.160-1896T>G		intron	N/A
	ELOVL2-AS1	NR_038964.1		n.362-1896T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2-AS1	ENST00000456616.2	TSL:1	n.397-1896T>G		intron	N/A
	ELOVL2-AS1	ENST00000456190.6	TSL:3	n.360-1896T>G		intron	N/A
	ELOVL2-AS1	ENST00000606532.6	TSL:4	n.329-1896T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63060 AN: 151892 Hom.: 13996 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.415 AC: 63106 AN: 152010 Hom.: 14015 Cov.: 32 AF XY: 0.421 AC XY: 31262 AN XY: 74268

African (AFR) AF: 0.280 AC: 11623 AN: 41482

American (AMR) AF: 0.547 AC: 8352 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3696 AN: 5152

South Asian (SAS) AF: 0.592 AC: 2856 AN: 4824

European-Finnish (FIN) AF: 0.433 AC: 4564 AN: 10548

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28810 AN: 67954

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.422 Hom.: 26692

Bravo AF: 0.415

Asia WGS AF: 0.620 AC: 2154 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1321535; hg19: chr6-11076026;