Genetic Variant ENSG00000297038:n.241+3323T>C (chr10-25816546-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000744909.1(ENSG00000297038):n.241+3323T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,996 control chromosomes in the GnomAD database, including 7,946 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 0.32 ( 7946 hom., cov: 31)

Consequence

ENSG00000297038
ENST00000744909.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.97

Publications

2 publications found

Variant links:

Genes affected

ENSG00000297038 (HGNC:):

ENSG00000297038 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 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
ENSG00000297038	ENST00000744909.1 link	n.241+3323T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48885

AN:

151882

Hom.:

7931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.422

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.330

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

GnomAD4 genome

AF:

0.322

AC:

48947

AN:

151996

Hom.:

7946

Cov.:

AF XY:

0.319

AC XY:

23685

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.323

AC:

13375

AN:

41464

American (AMR)

AF:

0.318

AC:

4858

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

903

AN:

3470

East Asian (EAS)

AF:

0.330

AC:

1700

AN:

5154

South Asian (SAS)

AF:

0.417

AC:

2001

AN:

4802

European-Finnish (FIN)

AF:

0.243

AC:

2573

AN:

10570

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.329

AC:

22350

AN:

67948

Other (OTH)

AF:

0.336

AC:

707

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1702

3403

5105

6806

8508

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<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:

0.330

Hom.:

2101

Bravo

AF:

0.326

Asia WGS

AF:

0.380

AC:

1321

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

3.0

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