Genetic Variant ENSG00000297913:n.108-6994T>C (chr1-159719533-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 ENST00000751816.1(ENSG00000297913):n.108-6994T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,150 control chromosomes in the GnomAD database, including 5,521 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 0.25 ( 5521 hom., cov: 32)

Consequence

ENSG00000297913
ENST00000751816.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Publications

13 publications found

Variant links:

Genes affected

ENSG00000297913 (HGNC:):

ENSG00000297913 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297913	ENST00000751816.1 link	n.108-6994T>C	intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1 link	n.110-6994T>C	intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1 link	n.63-6994T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38240

AN:

152032

Hom.:

5519

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.0612

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.314

Gnomad OTH

AF:

0.263

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

GnomAD4 genome

AF:

0.251

AC:

38265

AN:

152150

Hom.:

5521

Cov.:

AF XY:

0.253

AC XY:

18851

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.121

AC:

5033

AN:

41514

American (AMR)

AF:

0.304

AC:

4646

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.306

AC:

1064

AN:

3472

East Asian (EAS)

AF:

0.0611

AC:

317

AN:

5184

South Asian (SAS)

AF:

0.244

AC:

1179

AN:

4824

European-Finnish (FIN)

AF:

0.354

AC:

3742

AN:

10572

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.314

AC:

21339

AN:

67980

Other (OTH)

AF:

0.263

AC:

555

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1433

2866

4299

5732

7165

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.289

Hom.:

17892

Bravo

AF:

0.245

Asia WGS

AF:

0.163

AC:

570

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.0

(source)

DANN

Benign

0.82

PhyloP100

0.031

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