Variant 10-91410192-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_024467.1(HECTD2-AS1):n.427-59313C>T 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 0.188 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-AS1
NR_024467.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300

Variant links:

Genes affected

(HGNC:):

links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
HECTD2-AS1	NR_024467.1 linkuse as main transcript	n.427-59313C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein
	ENST00000688440.1 linkuse as main transcript	n.322-59313C>T	intron_variant, non_coding_transcript_variant
HECTD2	ENST00000631422.1 linkuse as main transcript	c.-184+771G>A	intron_variant	3	ENSP00000487686
	ENST00000700888.1 linkuse as main transcript	n.219-59313C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28427

AN:

151426

Hom.:

6269

Cov.:

show subpopulations

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:

AN:

232

Hom.:

AF XY:

0.0317

AC XY:

AN XY:

126

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0256

Gnomad4 NFE exome

AF:

0.0493

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.188

AC:

28488

AN:

151540

Hom.:

6289

Cov.:

AF XY:

0.183

AC XY:

13556

AN XY:

74094

show subpopulations

Gnomad4 AFR

AF:

0.537

Gnomad4 AMR

AF:

0.0846

Gnomad4 ASJ

AF:

0.0971

Gnomad4 EAS

AF:

0.0821

Gnomad4 SAS

AF:

0.0352

Gnomad4 FIN

AF:

0.0340

Gnomad4 NFE

AF:

0.0475

Gnomad4 OTH

AF:

0.149

Alfa

AF:

0.0211

Hom.:

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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over