rs7081363

Variant names:

• chr10-91410192-G-A
• rs7081363
• NM_001348365.2:c.-184+771G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-91410192-G-A
• chr10-91410192-G-C
• chr10-91410192-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001348365.2(HECTD2):​c.-184+771G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,772 control chromosomes in the GnomAD database, including 6,289 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 (6289 hom., cov: 32)
  • Exomes 𝑓: 0.043 (0 hom.)
• Consequence: HECTD2 NM_001348365.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 6 publications found

Genes affected

HECTD2 (HGNC:26736): (HECT domain E3 ubiquitin protein ligase 2) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in protein ubiquitination. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HECTD2	NM_182765.6	c.-247G>A		upstream_gene_variant		ENST00000298068.10	NP_877497.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HECTD2	ENST00000298068.10	c.-247G>A		upstream_gene_variant		1	NM_182765.6	ENSP00000298068.5

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28427 AN: 151426 Hom.: 6269 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.0431 AC: 10 AN: 232 Hom.: 0 AF XY: 0.0317 AC XY: 4 AN XY: 126

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.0256 AC: 2 AN: 78

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0493 AC: 7 AN: 142

Other (OTH) AF: 0.00 AC: 0 AN: 8

GnomAD4 genome AF: 0.188 AC: 28488 AN: 151540 Hom.: 6289 Cov.: 32 AF XY: 0.183 AC XY: 13556 AN XY: 74094

African (AFR) AF: 0.537 AC: 22218 AN: 41410

American (AMR) AF: 0.0846 AC: 1292 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 336 AN: 3462

East Asian (EAS) AF: 0.0821 AC: 420 AN: 5114

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4828

European-Finnish (FIN) AF: 0.0340 AC: 353 AN: 10384

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0475 AC: 3218 AN: 67774

Other (OTH) AF: 0.149 AC: 314 AN: 2102

Alfa AF: 0.0211 Hom.: 25

Bravo AF: 0.207

Asia WGS AF: 0.105 AC: 365 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.9
DANN	Benign	0.96
PhyloP100		-0.030
PromoterAI		-0.0051	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

Other links and lift over

dbSNP: rs7081363; hg19: chr10-93169949;