10-91588363-G-T

Position:

• chr10-91588363-G-T

Variant summary

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

The NR_024467.1(HECTD2-AS1):​n.110+22988C>A 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 0.269 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 NR_024467.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

HECTD2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HECTD2-AS1	NR_024467.1	n.110+22988C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.260

Alfa AF: 0.279 Hom.: 12380

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1329650; hg19: chr10-93348120;