Genetic Variant ENST00000736670.1:n.372-35903A>G (chr5-54902947-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000736670.1(ENSG00000296132):n.372-35903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,106 control chromosomes in the GnomAD database, including 45,210 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 0.77 ( 45210 hom., cov: 32)

Consequence

ENSG00000296132
ENST00000736670.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.425

Publications

6 publications found

Variant links:

Genes affected

ENSG00000296132 (HGNC:):

ENSG00000296132 links:

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new If you want to explore the variant's impact on the transcript ENST00000736670.1, 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736670.1. 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
ENSG00000296132	ENST00000736670.1	n.372-35903A>G	intron	N/A
ENSG00000296132	ENST00000736672.1	n.228+7481A>G	intron	N/A
ENSG00000296132	ENST00000736673.1	n.143+7481A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.770

AC:

116971

AN:

151988

Hom.:

45172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.808

Gnomad AMI

AF:

0.633

Gnomad AMR

AF:

0.796

Gnomad ASJ

AF:

0.758

Gnomad EAS

AF:

0.656

Gnomad SAS

AF:

0.747

Gnomad FIN

AF:

0.763

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.755

Gnomad OTH

AF:

0.764

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

GnomAD4 genome

AF:

0.770

AC:

117060

AN:

152106

Hom.:

45210

Cov.:

AF XY:

0.769

AC XY:

57130

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.808

AC:

33514

AN:

41502

American (AMR)

AF:

0.797

AC:

12181

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.758

AC:

2631

AN:

3472

East Asian (EAS)

AF:

0.655

AC:

3388

AN:

5172

South Asian (SAS)

AF:

0.746

AC:

3597

AN:

4822

European-Finnish (FIN)

AF:

0.763

AC:

8057

AN:

10560

Middle Eastern (MID)

AF:

0.728

AC:

214

AN:

294

European-Non Finnish (NFE)

AF:

0.755

AC:

51292

AN:

67974

Other (OTH)

AF:

0.763

AC:

1610

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1388

2775

4163

5550

6938

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<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:

0.754

Hom.:

14081

Bravo

AF:

0.774

Asia WGS

AF:

0.723

AC:

2513

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.2

(source)

DANN

Benign

0.79

PhyloP100

-0.42

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