dbSNP rs237131: ENSG00000304809:n.67-12720G>A (chr16-26629085-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 ENST00000806412.1(ENSG00000304809):n.67-12720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,128 control chromosomes in the GnomAD database, including 7,500 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 0.30 ( 7500 hom., cov: 32)

Consequence

ENSG00000304809
ENST00000806412.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.143

Publications

6 publications found

Variant links:

Genes affected

ENSG00000304809 (HGNC:):

ENSG00000304809 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000304809	ENST00000806412.1 link	n.67-12720G>A	intron_variant	Intron 1 of 1
ENSG00000304829	ENST00000806514.1 link	n.267-6782C>T	intron_variant	Intron 2 of 2
ENSG00000304829	ENST00000806515.1 link	n.71-6782C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

45022

AN:

152010

Hom.:

7504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.134

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.339

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.370

Gnomad OTH

AF:

0.339

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

GnomAD4 genome

AF:

0.296

AC:

45022

AN:

152128

Hom.:

7500

Cov.:

AF XY:

0.292

AC XY:

21675

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.134

AC:

5575

AN:

41522

American (AMR)

AF:

0.340

AC:

5196

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1383

AN:

3472

East Asian (EAS)

AF:

0.478

AC:

2467

AN:

5164

South Asian (SAS)

AF:

0.234

AC:

1129

AN:

4822

European-Finnish (FIN)

AF:

0.292

AC:

3086

AN:

10574

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.370

AC:

25171

AN:

67968

Other (OTH)

AF:

0.336

AC:

708

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1587

3175

4762

6350

7937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.351

Hom.:

42481

Bravo

AF:

0.298

Asia WGS

AF:

0.305

AC:

1062

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.90

(source)

DANN

Benign

0.40

PhyloP100

-0.14

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