Genetic Variant ENSG00000290870:n.2063-3665G>A (chr6-29861103-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000647952.1(ENSG00000290870):n.2063-3665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,166 control chromosomes in the GnomAD database, including 1,424 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 0.11 ( 1424 hom., cov: 31)

Consequence

ENSG00000290870
ENST00000647952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Publications

6 publications found

Variant links:

Genes affected

ENSG00000290870 (HGNC:):

ENSG00000290870 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1 link	n.2063-3665G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

16994

AN:

152048

Hom.:

1422

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.0749

Gnomad EAS

AF:

0.0245

Gnomad SAS

AF:

0.0676

Gnomad FIN

AF:

0.0525

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0535

Gnomad OTH

AF:

0.113

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

GnomAD4 genome

AF:

0.112

AC:

17011

AN:

152166

Hom.:

1424

Cov.:

AF XY:

0.111

AC XY:

8280

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.239

AC:

9908

AN:

41468

American (AMR)

AF:

0.126

AC:

1925

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0749

AC:

260

AN:

3472

East Asian (EAS)

AF:

0.0245

AC:

127

AN:

5182

South Asian (SAS)

AF:

0.0674

AC:

325

AN:

4822

European-Finnish (FIN)

AF:

0.0525

AC:

556

AN:

10598

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0535

AC:

3637

AN:

68010

Other (OTH)

AF:

0.111

AC:

234

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

704

1409

2113

2818

3522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<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:

0.0857

Hom.:

820

Bravo

AF:

0.126

Asia WGS

AF:

0.0510

AC:

177

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.9

(source)

DANN

Benign

0.63

PhyloP100

0.36

Splicing

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

Publications

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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