Genetic Variant ENSG00000297837:n.147+10616A>C (chr14-98309160-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 ENST00000751340.1(ENSG00000297837):n.147+10616A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,250 control chromosomes in the GnomAD database, including 1,163 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 0.11 ( 1163 hom., cov: 33)

Consequence

ENSG00000297837
ENST00000751340.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.311

Publications

2 publications found

Variant links:

Genes affected

ENSG00000297837 (HGNC:):

ENSG00000297837 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 = 0.172 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
ENSG00000297837	ENST00000751340.1 link	n.147+10616A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17206

AN:

152132

Hom.:

1163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.0162

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0825

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.113

AC:

17225

AN:

152250

Hom.:

1163

Cov.:

AF XY:

0.113

AC XY:

8445

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.176

AC:

7302

AN:

41536

American (AMR)

AF:

0.107

AC:

1630

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

356

AN:

3470

East Asian (EAS)

AF:

0.0162

AC:

AN:

5186

South Asian (SAS)

AF:

0.167

AC:

808

AN:

4832

European-Finnish (FIN)

AF:

0.108

AC:

1147

AN:

10602

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0825

AC:

5610

AN:

68000

Other (OTH)

AF:

0.107

AC:

227

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

769

1538

2307

3076

3845

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.0965

Hom.:

427

Bravo

AF:

0.115

Asia WGS

AF:

0.101

AC:

350

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.1

(source)

DANN

Benign

0.79

PhyloP100

0.31

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