6-114545699-G-T

Variant names:

• chr6-114545699-G-T
• rs786135
• ENST00000826283.1:n.668-2468G>T

Variant summary

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

The ENST00000826283.1(HDAC2-AS2):​n.668-2468G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,010 control chromosomes in the GnomAD database, including 25,082 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 0.56 (25082 hom., cov: 32)
• Consequence: HDAC2-AS2 ENST00000826283.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 2 publications found

Genes affected

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

LNCPOIR (HGNC:54521): (lncRNA periodontal mesenchymal stem cell osteogenesis related)

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 (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HDAC2-AS2	ENST00000826283.1	n.668-2468G>T		intron_variant	Intron 5 of 5
LNCPOIR	ENST00000826449.1	n.288-1778C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85499 AN: 151892 Hom.: 25038 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.563 AC: 85596 AN: 152010 Hom.: 25082 Cov.: 32 AF XY: 0.560 AC XY: 41585 AN XY: 74284

African (AFR) AF: 0.743 AC: 30825 AN: 41490

American (AMR) AF: 0.506 AC: 7731 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2739 AN: 5150

South Asian (SAS) AF: 0.601 AC: 2898 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4786 AN: 10562

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33358 AN: 67936

Other (OTH) AF: 0.523 AC: 1101 AN: 2106

Alfa AF: 0.525 Hom.: 7576

Bravo AF: 0.572

Asia WGS AF: 0.556 AC: 1935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.24
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs786135; hg19: chr6-114866863;