Genetic Variant ENSG00000298626:n.127-2261A>G (chr10-22809163-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000756997.1(ENSG00000298626):n.127-2261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,086 control chromosomes in the GnomAD database, including 14,349 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 0.41 ( 14349 hom., cov: 32)

Consequence

ENSG00000298626
ENST00000756997.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.302

Publications

4 publications found

Variant links:

Genes affected

ENSG00000298626 (HGNC:):

ENSG00000298626 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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
ENSG00000298626	ENST00000756997.1 link	n.127-2261A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61873

AN:

151968

Hom.:

14322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.641

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.385

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.557

Gnomad SAS

AF:

0.379

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.303

Gnomad OTH

AF:

0.400

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

GnomAD4 genome

AF:

0.407

AC:

61956

AN:

152086

Hom.:

14349

Cov.:

AF XY:

0.401

AC XY:

29796

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.641

AC:

26568

AN:

41446

American (AMR)

AF:

0.385

AC:

5884

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

959

AN:

3470

East Asian (EAS)

AF:

0.556

AC:

2878

AN:

5172

South Asian (SAS)

AF:

0.376

AC:

1811

AN:

4812

European-Finnish (FIN)

AF:

0.190

AC:

2008

AN:

10596

Middle Eastern (MID)

AF:

0.503

AC:

148

AN:

294

European-Non Finnish (NFE)

AF:

0.303

AC:

20616

AN:

67994

Other (OTH)

AF:

0.400

AC:

847

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1745

3491

5236

6982

8727

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

572

1144

1716

2288

2860

<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:

0.295

Hom.:

1856

Bravo

AF:

0.432

Asia WGS

AF:

0.441

AC:

1533

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.99

(source)

DANN

Benign

0.22

PhyloP100

-0.30

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