10-91590040-A-C

Position:

• chr10-91590040-A-C

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+21311T>G 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 0.189 in 151,898 control chromosomes in the GnomAD database, including 3,679 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 0.19 (3679 hom., cov: 32)
• Consequence: HECTD2-AS1 NR_024467.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

Genes affected

HECTD2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HECTD2-AS1	NR_024467.1	n.110+21311T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28739 AN: 151780 Hom.: 3683 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.189 AC: 28731 AN: 151898 Hom.: 3679 Cov.: 32 AF XY: 0.202 AC XY: 15009 AN XY: 74186

Gnomad4 AFR AF: 0.0854

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.184

Alfa AF: 0.178 Hom.: 2777

Bravo AF: 0.173

Asia WGS AF: 0.464 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1028936; hg19: chr10-93349797;