dbSNP rs736839: ENSG00000309250:n.129+19709G>A (chr18-49001695-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000839810.1(ENSG00000309250):n.129+19709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,104 control chromosomes in the GnomAD database, including 6,383 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 0.28 ( 6383 hom., cov: 33)

Consequence

ENSG00000309250
ENST00000839810.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0430

Publications

6 publications found

Variant links:

Genes affected

ENSG00000309250 (HGNC:):

ENSG00000309250 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000309250	ENST00000839810.1 link	n.129+19709G>A	intron_variant	Intron 1 of 2
ENSG00000309250	ENST00000839811.1 link	n.129+19709G>A	intron_variant	Intron 1 of 1
ENSG00000309250	ENST00000839812.1 link	n.294-5902G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42579

AN:

151986

Hom.:

6380

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.530

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.269

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

GnomAD4 genome

AF:

0.280

AC:

42609

AN:

152104

Hom.:

6383

Cov.:

AF XY:

0.286

AC XY:

21261

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.187

AC:

7775

AN:

41492

American (AMR)

AF:

0.341

AC:

5219

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.243

AC:

842

AN:

3472

East Asian (EAS)

AF:

0.531

AC:

2736

AN:

5156

South Asian (SAS)

AF:

0.322

AC:

1551

AN:

4822

European-Finnish (FIN)

AF:

0.311

AC:

3292

AN:

10586

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.299

AC:

20312

AN:

67968

Other (OTH)

AF:

0.267

AC:

564

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1555

3110

4664

6219

7774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.291

Hom.:

20862

Bravo

AF:

0.278

Asia WGS

AF:

0.391

AC:

1359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

6.9

(source)

DANN

Benign

0.82

PhyloP100

0.043

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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