rs11591635

Variant names:

• chr10-91600545-T-C
• rs11591635
• ENST00000838016.1:n.166+13081A>G

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+13081A>G variant causes a intron 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 ENST00000838016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 2 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=-0.93).
• 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 rank	MANE	Protein	UniProt
HECTD2-AS1	NR_024467.1	n.110+10806A>G		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+13081A>G		intron_variant	Intron 1 of 3
HECTD2-AS1	ENST00000838017.1	n.250+10712A>G		intron_variant	Intron 1 of 3
HECTD2-AS1	ENST00000838018.1	n.127+10806A>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.188 AC: 7810 AN: 41478

American (AMR) AF: 0.137 AC: 2101 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0661 AC: 229 AN: 3466

East Asian (EAS) AF: 0.108 AC: 557 AN: 5142

South Asian (SAS) AF: 0.115 AC: 555 AN: 4806

European-Finnish (FIN) AF: 0.0898 AC: 950 AN: 10576

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0856 AC: 5820 AN: 67974

Other (OTH) AF: 0.112 AC: 238 AN: 2116

Alfa AF: 0.0957 Hom.: 2394

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11591635; hg19: chr10-93360302;