Genetic Variant ENSG00000290870:n.2156-1998C>T (chr6-29854484-G-A) – 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.2156-1998C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,418 control chromosomes in the GnomAD database, including 5,347 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 ( 5347 hom., cov: 32)

Consequence

ENSG00000290870
ENST00000647952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00200

Publications

36 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375010	XR_926680.3 link	n.42-1998C>T	intron_variant	Intron 1 of 2
LOC105375010	XR_926681.2 link	n.42-1998C>T	intron_variant	Intron 1 of 3
LOC105375010	XR_926682.3 link	n.42-1998C>T	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1 link	n.2156-1998C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

38917

AN:

151296

Hom.:

5345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.352

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.232

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

GnomAD4 genome

AF:

0.257

AC:

38926

AN:

151418

Hom.:

5347

Cov.:

AF XY:

0.256

AC XY:

18957

AN XY:

74052

show subpopulations

African (AFR)

AF:

0.191

AC:

7890

AN:

41360

American (AMR)

AF:

0.235

AC:

3580

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.170

AC:

591

AN:

3470

East Asian (EAS)

AF:

0.352

AC:

1820

AN:

5164

South Asian (SAS)

AF:

0.152

AC:

732

AN:

4800

European-Finnish (FIN)

AF:

0.336

AC:

3527

AN:

10508

Middle Eastern (MID)

AF:

0.160

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.295

AC:

19940

AN:

67590

Other (OTH)

AF:

0.230

AC:

483

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1446

2893

4339

5786

7232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<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:

0.276

Hom.:

14769

Bravo

AF:

0.252

Asia WGS

AF:

0.195

AC:

677

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

7.8

(source)

DANN

Benign

0.20

PhyloP100

0.0020

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