10-91588363-G-T

Variant names:

• chr10-91588363-G-T
• rs1329650
• ENST00000838016.1:n.166+25263C>A

Variant summary

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

The ENST00000838016.1(HECTD2-AS1):​n.166+25263C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,032 control chromosomes in the GnomAD database, including 7,138 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 0.27 (7138 hom., cov: 32)
• Consequence: HECTD2-AS1 ENST00000838016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 49 publications found

Genes affected

HECTD2-AS1 (HGNC:):

HECTD2-AS1 (HGNC:48679): (HECTD2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HECTD2-AS1	NR_024467.1	n.110+22988C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HECTD2-AS1	ENST00000838016.1	n.166+25263C>A		intron_variant	Intron 1 of 3
HECTD2-AS1	ENST00000838017.1	n.250+22894C>A		intron_variant	Intron 1 of 3
HECTD2-AS1	ENST00000838018.1	n.127+22988C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40911 AN: 151912 Hom.: 7134 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.269 AC: 40915 AN: 152032 Hom.: 7138 Cov.: 32 AF XY: 0.284 AC XY: 21075 AN XY: 74308

African (AFR) AF: 0.101 AC: 4171 AN: 41494

American (AMR) AF: 0.326 AC: 4979 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3743 AN: 5176

South Asian (SAS) AF: 0.577 AC: 2782 AN: 4822

European-Finnish (FIN) AF: 0.419 AC: 4414 AN: 10542

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.279 AC: 18971 AN: 67956

Other (OTH) AF: 0.260 AC: 546 AN: 2096

Alfa AF: 0.280 Hom.: 28093

Bravo AF: 0.251

Asia WGS AF: 0.589 AC: 2049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.086
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1329650; hg19: chr10-93348120;