Genetic Variant ENST00000740833.1:n.406+15204G>C (chr7-76713262-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000740833.1(ENSG00000296620):n.406+15204G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,964 control chromosomes in the GnomAD database, including 4,213 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 0.23 ( 4213 hom., cov: 31)

Consequence

ENSG00000296620
ENST00000740833.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.213

Publications

6 publications found

Variant links:

Genes affected

ENSG00000296620 (HGNC:):

ENSG00000296620 links:

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new If you want to explore the variant's impact on the transcript ENST00000740833.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.52).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740833.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000296620	ENST00000740833.1	n.406+15204G>C	intron	N/A
ENSG00000296620	ENST00000740834.1	n.515+15204G>C	intron	N/A
ENSG00000296620	ENST00000740835.1	n.202+15482G>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34297

AN:

151846

Hom.:

4209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.0168

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.254

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

GnomAD4 genome

AF:

0.226

AC:

34322

AN:

151964

Hom.:

4213

Cov.:

AF XY:

0.226

AC XY:

16755

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.137

AC:

5684

AN:

41418

American (AMR)

AF:

0.268

AC:

4088

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

1029

AN:

3466

East Asian (EAS)

AF:

0.0168

AC:

AN:

5174

South Asian (SAS)

AF:

0.243

AC:

1171

AN:

4812

European-Finnish (FIN)

AF:

0.233

AC:

2455

AN:

10552

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.278

AC:

18893

AN:

67970

Other (OTH)

AF:

0.251

AC:

528

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1251

2502

3752

5003

6254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<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:

0.0865

Hom.:

147

Bravo

AF:

0.222

Asia WGS

AF:

0.124

AC:

430

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

-0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over