Genetic Variant ENSG00000290870:n.2063-3445T>C (chr6-29860883-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.2063-3445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,026 control chromosomes in the GnomAD database, including 5,338 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 0.26 ( 5338 hom., cov: 32)

Consequence

ENSG00000290870
ENST00000647952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.429

Publications

56 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 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.2063-3445T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39358

AN:

151908

Hom.:

5336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.353

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.236

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

GnomAD4 genome

AF:

0.259

AC:

39365

AN:

152026

Hom.:

5338

Cov.:

AF XY:

0.258

AC XY:

19151

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.192

AC:

7974

AN:

41456

American (AMR)

AF:

0.237

AC:

3616

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

592

AN:

3470

East Asian (EAS)

AF:

0.353

AC:

1827

AN:

5170

South Asian (SAS)

AF:

0.154

AC:

740

AN:

4808

European-Finnish (FIN)

AF:

0.338

AC:

3567

AN:

10568

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.297

AC:

20192

AN:

67956

Other (OTH)

AF:

0.233

AC:

492

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1499

2998

4497

5996

7495

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

392

784

1176

1568

1960

<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:

0.282

Hom.:

23215

Bravo

AF:

0.252

Asia WGS

AF:

0.196

AC:

682

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.7

(source)

DANN

Benign

0.53

PhyloP100

0.43

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