6-114351790-G-T

Variant names:

• chr6-114351790-G-T
• rs1407728
• ENST00000518470.5:n.291+11175G>T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC107986638 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986638	XR_002956366.2	n.65+9401G>T		intron_variant	Intron 1 of 7
LOC107986638	XR_002956367.1	n.65+9401G>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HDAC2-AS2	ENST00000518470.5	n.291+11175G>T		intron_variant	Intron 2 of 5	4

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

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.00404

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0402 Hom.: 111

Bravo AF: 0.0794

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1407728; hg19: chr6-114672954;