Genetic Variant ENST00000838016.1:n.166+23586T>G (chr10-91590040-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000838016.1(HECTD2-AS1):n.166+23586T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,898 control chromosomes in the GnomAD database, including 3,679 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 ( 3679 hom., cov: 32)

Consequence

HECTD2-AS1
ENST00000838016.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.401

Publications

16 publications found

Variant links:

Genes affected

HECTD2-AS1 (HGNC:):

HECTD2-AS1 links:

HECTD2-AS1 (HGNC:48679): (HECTD2 antisense RNA 1)

HECTD2-AS1 links:

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new If you want to explore the variant's impact on the transcript ENST00000838016.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HECTD2-AS1	NR_024467.1		n.110+21311T>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
HECTD2-AS1	ENST00000838016.1	n.166+23586T>G	intron	N/A
HECTD2-AS1	ENST00000838017.1	n.250+21217T>G	intron	N/A
HECTD2-AS1	ENST00000838018.1	n.127+21311T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28739

AN:

151780

Hom.:

3683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0855

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.612

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.309

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.189

AC:

28731

AN:

151898

Hom.:

3679

Cov.:

AF XY:

0.202

AC XY:

15009

AN XY:

74186

show subpopulations

African (AFR)

AF:

0.0854

AC:

3539

AN:

41460

American (AMR)

AF:

0.209

AC:

3193

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.225

AC:

782

AN:

3468

East Asian (EAS)

AF:

0.612

AC:

3141

AN:

5132

South Asian (SAS)

AF:

0.447

AC:

2144

AN:

4796

European-Finnish (FIN)

AF:

0.309

AC:

3245

AN:

10508

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.177

AC:

12059

AN:

67950

Other (OTH)

AF:

0.184

AC:

390

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1093

2186

3280

4373

5466

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.180

Hom.:

7949

Bravo

AF:

0.173

Asia WGS

AF:

0.464

AC:

1612

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.73

(source)

DANN

Benign

0.62

PhyloP100

-0.40

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over