Genetic Variant ENSG00000297825:n.87-261T>C (chr9-111855741-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000751282.1(ENSG00000297825):n.87-261T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,156 control chromosomes in the GnomAD database, including 1,597 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 0.14 ( 1597 hom., cov: 32)

Consequence

ENSG00000297825
ENST00000751282.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.489

Publications

2 publications found

Variant links:

Genes affected

ENSG00000297825 (HGNC:):

ENSG00000297825 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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
ENSG00000297825	ENST00000751282.1 link	n.87-261T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21602

AN:

152038

Hom.:

1597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.0940

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.0241

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.131

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

GnomAD4 genome

AF:

0.142

AC:

21619

AN:

152156

Hom.:

1597

Cov.:

AF XY:

0.140

AC XY:

10390

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.162

AC:

6719

AN:

41508

American (AMR)

AF:

0.0939

AC:

1435

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

525

AN:

3470

East Asian (EAS)

AF:

0.0239

AC:

124

AN:

5178

South Asian (SAS)

AF:

0.135

AC:

649

AN:

4824

European-Finnish (FIN)

AF:

0.148

AC:

1564

AN:

10590

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10160

AN:

67980

Other (OTH)

AF:

0.128

AC:

270

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

952

1904

2855

3807

4759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.143

Hom.:

875

Bravo

AF:

0.140

Asia WGS

AF:

0.0800

AC:

280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.3

(source)

DANN

Benign

0.69

PhyloP100

0.49

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