dbSNP rs114646238: ENSG00000309145:n.435-18799T>C (chr4-130105333-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000839037.1(ENSG00000309145):n.435-18799T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0461 in 152,208 control chromosomes in the GnomAD database, including 226 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 0.046 ( 226 hom., cov: 32)

Consequence

ENSG00000309145
ENST00000839037.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159

Publications

1 publications found

Variant links:

Genes affected

ENSG00000309145 (HGNC:):

ENSG00000309145 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0715 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
ENSG00000309145	ENST00000839037.1 link	n.435-18799T>C		intron_variant	Intron 4 of 5
ENSG00000309145	ENST00000839038.1 link	n.431+13895T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0461

AC:

7011

AN:

152090

Hom.:

226

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0124

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0242

Gnomad ASJ

AF:

0.0245

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0189

Gnomad FIN

AF:

0.0837

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0731

Gnomad OTH

AF:

0.0278

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

GnomAD4 genome

AF:

0.0461

AC:

7010

AN:

152208

Hom.:

226

Cov.:

AF XY:

0.0457

AC XY:

3401

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0124

AC:

515

AN:

41576

American (AMR)

AF:

0.0241

AC:

369

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0245

AC:

AN:

3472

East Asian (EAS)

AF:

0.000387

AC:

AN:

5170

South Asian (SAS)

AF:

0.0189

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0837

AC:

888

AN:

10608

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0732

AC:

4971

AN:

67954

Other (OTH)

AF:

0.0275

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

343

687

1030

1374

1717

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0430

Hom.:

Bravo

AF:

0.0392

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

4.4

(source)

DANN

Benign

0.29

PhyloP100

0.16

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