Genetic Variant ENSG00000293725:n.66+25899A>G (chr10-121259506-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 ENST00000718585.1(ENSG00000293725):n.66+25899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,056 control chromosomes in the GnomAD database, including 26,705 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 0.59 ( 26705 hom., cov: 32)

Consequence

ENSG00000293725
ENST00000718585.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.692

Publications

2 publications found

Variant links:

Genes affected

ENSG00000293725 (HGNC:):

ENSG00000293725 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=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378523	XR_007062321.1 link	n.515+53710A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293725	ENST00000718585.1 link	n.66+25899A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.588

AC:

89290

AN:

151938

Hom.:

26688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.475

Gnomad AMI

AF:

0.605

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.649

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.792

Gnomad FIN

AF:

0.577

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.632

Gnomad OTH

AF:

0.588

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

GnomAD4 genome

AF:

0.588

AC:

89340

AN:

152056

Hom.:

26705

Cov.:

AF XY:

0.588

AC XY:

43722

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.474

AC:

19659

AN:

41456

American (AMR)

AF:

0.615

AC:

9388

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.649

AC:

2252

AN:

3470

East Asian (EAS)

AF:

0.611

AC:

3159

AN:

5170

South Asian (SAS)

AF:

0.793

AC:

3819

AN:

4816

European-Finnish (FIN)

AF:

0.577

AC:

6098

AN:

10574

Middle Eastern (MID)

AF:

0.643

AC:

189

AN:

294

European-Non Finnish (NFE)

AF:

0.632

AC:

42972

AN:

67990

Other (OTH)

AF:

0.593

AC:

1253

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1869

3737

5606

7474

9343

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.470

Hom.:

1614

Bravo

AF:

0.583

Asia WGS

AF:

0.693

AC:

2408

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.0

(source)

DANN

Benign

0.42

PhyloP100

0.69

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