6-114027356-T-C

Variant summary

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

The NR_125845.1(HDAC2-AS2):n.1310+31296T>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 0.315 in 152,106 control chromosomes in the GnomAD database, including 7,668 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 0.32 (7668 hom., cov: 32)
• Consequence: HDAC2-AS2 NR_125845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HDAC2-AS2	NR_125845.1	n.1310+31296T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HDAC2-AS2	ENST00000519104.5	n.1310+31296T>C		intron_variant, non_coding_transcript_variant		1
HDAC2-AS2	ENST00000519270.1	n.87-31275T>C		intron_variant, non_coding_transcript_variant		4
HDAC2-AS2	ENST00000523087.1	n.106+31296T>C		intron_variant, non_coding_transcript_variant		3
HDAC2-AS2	ENST00000691803.1	n.69-20535T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47934 AN: 151988 Hom.: 7665 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.315 AC: 47939 AN: 152106 Hom.: 7668 Cov.: 32 AF XY: 0.313 AC XY: 23281 AN XY: 74354

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.307

Alfa AF: 0.317 Hom.: 13364

Bravo AF: 0.305

Asia WGS AF: 0.203 AC: 705 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	3.9
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11752866; hg19: chr6-114348520;