dbSNP rs4833233: PP12613:n.241-767G>A (chr4-121767589-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000746424.1(PP12613):n.241-767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,770 control chromosomes in the GnomAD database, including 20,377 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 ( 20377 hom., cov: 30)

Consequence

PP12613
ENST00000746424.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.503

Publications

12 publications found

Variant links:

Genes affected

PP12613 (HGNC:):

PP12613 links:

Genome browser will be placed here

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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PP12613	ENST00000746424.1 link	n.241-767G>A	intron_variant	Intron 1 of 1
PP12613	ENST00000746425.1 link	n.239-773G>A	intron_variant	Intron 1 of 1
PP12613	ENST00000746426.1 link	n.235-183G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78193

AN:

151652

Hom.:

20361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.550

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.562

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.495

Gnomad OTH

AF:

0.512

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

GnomAD4 genome

AF:

0.516

AC:

78262

AN:

151770

Hom.:

20377

Cov.:

AF XY:

0.515

AC XY:

38153

AN XY:

74152

show subpopulations

African (AFR)

AF:

0.558

AC:

23055

AN:

41346

American (AMR)

AF:

0.550

AC:

8402

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.530

AC:

1837

AN:

3468

East Asian (EAS)

AF:

0.430

AC:

2215

AN:

5156

South Asian (SAS)

AF:

0.562

AC:

2688

AN:

4784

European-Finnish (FIN)

AF:

0.451

AC:

4733

AN:

10490

Middle Eastern (MID)

AF:

0.541

AC:

159

AN:

294

European-Non Finnish (NFE)

AF:

0.496

AC:

33664

AN:

67938

Other (OTH)

AF:

0.511

AC:

1078

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1915

3830

5744

7659

9574

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

688

1376

2064

2752

3440

<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:

0.508

Hom.:

62948

Bravo

AF:

0.524

Asia WGS

AF:

0.515

AC:

1792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.50

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