Genetic Variant ENSG00000250258:n.125+197T>G (chr5-79803641-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000421252.2(ENSG00000250258):n.125+197T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,118 control chromosomes in the GnomAD database, including 6,885 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 ( 6885 hom., cov: 31)

Consequence

ENSG00000250258
ENST00000421252.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0230

Publications

7 publications found

Variant links:

Genes affected

ENSG00000250258 (HGNC:):

ENSG00000250258 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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
ENSG00000250258	ENST00000421252.2 link	n.125+197T>G		intron_variant	Intron 2 of 4	3
ENSG00000286818	ENST00000827626.1 link	n.83+1887A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41564

AN:

152000

Hom.:

6884

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.382

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.283

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

GnomAD4 genome

AF:

0.273

AC:

41553

AN:

152118

Hom.:

6885

Cov.:

AF XY:

0.269

AC XY:

20015

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.103

AC:

4266

AN:

41536

American (AMR)

AF:

0.260

AC:

3973

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.340

AC:

1182

AN:

3472

East Asian (EAS)

AF:

0.101

AC:

525

AN:

5180

South Asian (SAS)

AF:

0.286

AC:

1375

AN:

4814

European-Finnish (FIN)

AF:

0.317

AC:

3354

AN:

10566

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.381

AC:

25862

AN:

67968

Other (OTH)

AF:

0.278

AC:

588

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1441

2882

4324

5765

7206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.329

Hom.:

17444

Bravo

AF:

0.258

Asia WGS

AF:

0.165

AC:

572

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.7

(source)

DANN

Benign

0.75

PhyloP100

-0.023

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