chr6-114351790-G-T

Variant names:

• chr6-114351790-G-T
• rs1407728
• ENST00000518470.5:n.291+11175G>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.291+11175G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 152,140 control chromosomes in the GnomAD database, including 1,139 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 0.065 (1139 hom., cov: 32)
• Consequence: HDAC2-AS2 ENST00000518470.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HDAC2-AS2	ENST00000518470.5	TSL:4	n.291+11175G>T		intron	N/A
	HDAC2-AS2	ENST00000826280.1		n.175+10366G>T		intron	N/A
	HDAC2-AS2	ENST00000826281.1		n.170+10366G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0653 AC: 9925 AN: 152022 Hom.: 1137 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00404

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0654 AC: 9943 AN: 152140 Hom.: 1139 Cov.: 32 AF XY: 0.0721 AC XY: 5362 AN XY: 74362

African (AFR) AF: 0.0836 AC: 3471 AN: 41500

American (AMR) AF: 0.152 AC: 2319 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2741 AN: 5146

South Asian (SAS) AF: 0.0432 AC: 208 AN: 4820

European-Finnish (FIN) AF: 0.0574 AC: 608 AN: 10592

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00404 AC: 275 AN: 68020

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0311 Hom.: 1089

Bravo AF: 0.0794

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.33
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs1407728; hg19: chr6-114672954;