rs760609

Variant names:

• chr6-114386936-A-C
• rs760609
• ENST00000518470.5:n.392+15244A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-114386936-A-C
• chr6-114386936-A-G
• chr6-114386936-A-T

Variant summary

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

The ENST00000518470.5(HDAC2-AS2):​n.392+15244A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,688 control chromosomes in the GnomAD database, including 26,891 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 (26891 hom., cov: 30)
• Consequence: HDAC2-AS2 ENST00000518470.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 2 publications found

Genes affected

HDAC2-AS2 (HGNC:43590): (HDAC2 and HS3ST5 antisense RNA 2)

LOC107986638 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518470.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDAC2-AS2	ENST00000518470.5	TSL:4	n.392+15244A>C		intron	N/A
	HDAC2-AS2	ENST00000826280.1		n.276+15244A>C		intron	N/A
	HDAC2-AS2	ENST00000826281.1		n.171-8278A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89612 AN: 151570 Hom.: 26857 Cov.: 30

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.591 AC: 89701 AN: 151688 Hom.: 26891 Cov.: 30 AF XY: 0.596 AC XY: 44147 AN XY: 74110

African (AFR) AF: 0.568 AC: 23479 AN: 41350

American (AMR) AF: 0.677 AC: 10313 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1940 AN: 3464

East Asian (EAS) AF: 0.833 AC: 4262 AN: 5114

South Asian (SAS) AF: 0.656 AC: 3154 AN: 4810

European-Finnish (FIN) AF: 0.599 AC: 6289 AN: 10504

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38473 AN: 67900

Other (OTH) AF: 0.583 AC: 1225 AN: 2102

Alfa AF: 0.581 Hom.: 13150

Bravo AF: 0.599

Asia WGS AF: 0.746 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs760609;

hg19: chr6-114708100;