Genetic Variant ENSG00000297356:n.667+8574T>C (chr3-72629872-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000747314.1(ENSG00000297356):n.667+8574T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,134 control chromosomes in the GnomAD database, including 20,675 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 0.52 ( 20675 hom., cov: 33)

Consequence

ENSG00000297356
ENST00000747314.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.846

Publications

3 publications found

Variant links:

Genes affected

ENSG00000297356 (HGNC:):

ENSG00000297356 links:

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new If you want to explore the variant's impact on the transcript ENST00000747314.1, 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747314.1. 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297356	ENST00000747314.1		n.667+8574T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.518

AC:

78808

AN:

152016

Hom.:

20649

Cov.:

show subpopulations

Gnomad AFR

AF:

0.542

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.568

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.640

Gnomad SAS

AF:

0.629

Gnomad FIN

AF:

0.461

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.526

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

GnomAD4 genome

AF:

0.518

AC:

78879

AN:

152134

Hom.:

20675

Cov.:

AF XY:

0.523

AC XY:

38889

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.543

AC:

22533

AN:

41520

American (AMR)

AF:

0.568

AC:

8693

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.581

AC:

2014

AN:

3466

East Asian (EAS)

AF:

0.641

AC:

3305

AN:

5160

South Asian (SAS)

AF:

0.628

AC:

3031

AN:

4824

European-Finnish (FIN)

AF:

0.461

AC:

4874

AN:

10574

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.481

AC:

32727

AN:

67984

Other (OTH)

AF:

0.527

AC:

1112

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2000

4001

6001

8002

10002

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<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:

0.424

Hom.:

1896

Bravo

AF:

0.523

Asia WGS

AF:

0.646

AC:

2246

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.97

(source)

DANN

Benign

0.71

PhyloP100

-0.85

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