Genetic Variant ENSG00000290870:n.2063-3757T>C (chr6-29861195-A-G) – 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.2063-3757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,988 control chromosomes in the GnomAD database, including 5,959 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 0.27 ( 5959 hom., cov: 31)

Consequence

ENSG00000290870
ENST00000647952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.413

Publications

11 publications found

Variant links:

Genes affected

ENSG00000290870 (HGNC:):

ENSG00000290870 links:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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.2063-3757T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40599

AN:

151870

Hom.:

5948

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.196

Gnomad OTH

AF:

0.281

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

GnomAD4 genome

AF:

0.267

AC:

40632

AN:

151988

Hom.:

5959

Cov.:

AF XY:

0.268

AC XY:

19924

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.389

AC:

16105

AN:

41406

American (AMR)

AF:

0.328

AC:

5004

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

814

AN:

3468

East Asian (EAS)

AF:

0.244

AC:

1262

AN:

5180

South Asian (SAS)

AF:

0.259

AC:

1251

AN:

4826

European-Finnish (FIN)

AF:

0.190

AC:

2003

AN:

10554

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.196

AC:

13346

AN:

67968

Other (OTH)

AF:

0.285

AC:

601

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1459

2918

4376

5835

7294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.259

Hom.:

3747

Bravo

AF:

0.286

Asia WGS

AF:

0.323

AC:

1124

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.3

(source)

DANN

Benign

0.80

PhyloP100

0.41

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