rs760609

chr6-114386936-A-Cchr6-114386936-A-Gchr6-114386936-A-T

Variant summary

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

The XR_002956366.2(LOC107986638):n.167-8278A>C variant causes a intron, non coding transcript 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: LOC107986638 XR_002956366.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

Genes affected

LOC107986638 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986638	XR_002956366.2	n.167-8278A>C		intron_variant, non_coding_transcript_variant
LOC107986638	XR_002956367.1	n.167-8278A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HDAC2-AS2	ENST00000518470.5	n.392+15244A>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.583

Alfa AF: 0.581 Hom.: 11710

Bravo AF: 0.599

Asia WGS AF: 0.746 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760609; hg19: chr6-114708100;