Genetic Variant ENSG00000259097:n.121+1202T>G (chr14-98203821-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 ENST00000555776.1(ENSG00000259097):n.121+1202T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,036 control chromosomes in the GnomAD database, including 25,932 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 0.58 ( 25932 hom., cov: 32)

Consequence

ENSG00000259097
ENST00000555776.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Publications

8 publications found

Variant links:

Genes affected

ENSG00000259097 (HGNC:):

ENSG00000259097 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987207	XR_001750875.2 link	n.134-654T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000259097	ENST00000555776.1 link	n.121+1202T>G	intron_variant	Intron 1 of 2	4
ENSG00000259097	ENST00000702227.2 link	n.135-654T>G	intron_variant	Intron 1 of 2
ENSG00000259097	ENST00000733052.1 link	n.120+1202T>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.581

AC:

88304

AN:

151918

Hom.:

25896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.615

Gnomad AMI

AF:

0.457

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.522

Gnomad EAS

AF:

0.767

Gnomad SAS

AF:

0.611

Gnomad FIN

AF:

0.594

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.554

Gnomad OTH

AF:

0.591

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

GnomAD4 genome

AF:

0.581

AC:

88392

AN:

152036

Hom.:

25932

Cov.:

AF XY:

0.583

AC XY:

43309

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.616

AC:

25529

AN:

41472

American (AMR)

AF:

0.549

AC:

8393

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.522

AC:

1810

AN:

3470

East Asian (EAS)

AF:

0.767

AC:

3960

AN:

5166

South Asian (SAS)

AF:

0.608

AC:

2924

AN:

4810

European-Finnish (FIN)

AF:

0.594

AC:

6275

AN:

10558

Middle Eastern (MID)

AF:

0.602

AC:

177

AN:

294

European-Non Finnish (NFE)

AF:

0.554

AC:

37652

AN:

67966

Other (OTH)

AF:

0.595

AC:

1255

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1931

3862

5792

7723

9654

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<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:

0.561

Hom.:

72674

Bravo

AF:

0.583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.6

(source)

DANN

Benign

0.42

PhyloP100

-0.17

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