Genetic Variant HEATR3-AS1:n.380+2472G>C (chr16-50062219-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000568130.3(HEATR3-AS1):n.380+2472G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,188 control chromosomes in the GnomAD database, including 2,588 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 0.15 ( 2588 hom., cov: 33)

Consequence

HEATR3-AS1
ENST00000568130.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.442

Publications

5 publications found

Variant links:

Genes affected

HEATR3-AS1 (HGNC:55406): (HEATR3 antisense RNA 1)

HEATR3-AS1 links:

Genome browser will be placed here

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HEATR3-AS1	NR_186390.1 link	n.389+2472G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HEATR3-AS1	ENST00000568130.3 link	n.380+2472G>C	intron_variant	Intron 2 of 2	3
HEATR3-AS1	ENST00000719503.1 link	n.259+3834G>C	intron_variant	Intron 1 of 1
HEATR3-AS1	ENST00000719504.1 link	n.270+3834G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23157

AN:

152070

Hom.:

2589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.0487

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.0988

Gnomad FIN

AF:

0.0460

Gnomad MID

AF:

0.0764

Gnomad NFE

AF:

0.0792

Gnomad OTH

AF:

0.125

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

GnomAD4 genome

AF:

0.152

AC:

23195

AN:

152188

Hom.:

2588

Cov.:

AF XY:

0.150

AC XY:

11150

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.318

AC:

13203

AN:

41492

American (AMR)

AF:

0.118

AC:

1810

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0487

AC:

169

AN:

3470

East Asian (EAS)

AF:

0.259

AC:

1341

AN:

5184

South Asian (SAS)

AF:

0.0979

AC:

473

AN:

4832

European-Finnish (FIN)

AF:

0.0460

AC:

487

AN:

10590

Middle Eastern (MID)

AF:

0.0685

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0792

AC:

5387

AN:

68016

Other (OTH)

AF:

0.126

AC:

267

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

922

1845

2767

3690

4612

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.117

Hom.:

222

Bravo

AF:

0.169

Asia WGS

AF:

0.167

AC:

581

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.7

(source)

DANN

Benign

0.31

PhyloP100

0.44

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over