rs11591635

chr10-91600545-T-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+10806A>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 0.12 in 152,050 control chromosomes in the GnomAD database, including 1,252 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 0.12 (1252 hom., cov: 32)
• Consequence: HECTD2-AS1 NR_024467.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

HECTD2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HECTD2-AS1	NR_024467.1	n.110+10806A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18265 AN: 151932 Hom.: 1251 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0661

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0856

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.120 AC: 18294 AN: 152050 Hom.: 1252 Cov.: 32 AF XY: 0.120 AC XY: 8918 AN XY: 74308

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0661

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.0856

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0901 Hom.: 1392

Bravo AF: 0.127

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11591635; hg19: chr10-93360302;