rs1329650

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-91588363-G-A
• chr10-91588363-G-C
• chr10-91588363-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000838016.1(HECTD2-AS1):​n.166+25263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000237 in 152,096 control chromosomes in the GnomAD database, including 1 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 0.00024 (1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HECTD2-AS1	NR_024467.1	n.110+22988C>T		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>T		intron_variant	Intron 1 of 3
HECTD2-AS1	ENST00000838017.1	n.250+22894C>T		intron_variant	Intron 1 of 3
HECTD2-AS1	ENST00000838018.1	n.127+22988C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.000237 AC: 36 AN: 151978 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00210

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.000964

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

GnomAD4 genome AF: 0.000237 AC: 36 AN: 152096 Hom.: 1 Cov.: 32 AF XY: 0.000282 AC XY: 21 AN XY: 74342

African (AFR) AF: 0.00 AC: 0 AN: 41514

American (AMR) AF: 0.00209 AC: 32 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10554

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 67976

Other (OTH) AF: 0.000954 AC: 2 AN: 2096

Alfa AF: 0.00 Hom.: 28093

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.40
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;