dbSNP rs6457594: ENSG00000307923:n.273+1975A>G (chr6-32476184-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000829864.1(ENSG00000307923):n.273+1975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.68 ( 28162 hom., cov: 39)

Failed GnomAD Quality Control

Consequence

ENSG00000307923
ENST00000829864.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.99

Publications

7 publications found

Variant links:

Genes affected

ENSG00000307923 (HGNC:):

ENSG00000307923 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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
ENSG00000307923	ENST00000829864.1 link	n.273+1975A>G		intron_variant	Intron 2 of 2
ENSG00000307923	ENST00000829865.1 link	n.269+1975A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.676

AC:

100097

AN:

148098

Hom.:

28143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.615

Gnomad AMI

AF:

0.753

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.720

Gnomad EAS

AF:

0.610

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.784

Gnomad MID

AF:

0.643

Gnomad NFE

AF:

0.691

Gnomad OTH

AF:

0.684

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.676

AC:

100165

AN:

148212

Hom.:

28162

Cov.:

AF XY:

0.677

AC XY:

49095

AN XY:

72470

show subpopulations

African (AFR)

AF:

0.615

AC:

24451

AN:

39754

American (AMR)

AF:

0.714

AC:

10713

AN:

15014

Ashkenazi Jewish (ASJ)

AF:

0.720

AC:

2473

AN:

3436

East Asian (EAS)

AF:

0.611

AC:

3065

AN:

5016

South Asian (SAS)

AF:

0.635

AC:

2992

AN:

4714

European-Finnish (FIN)

AF:

0.784

AC:

8171

AN:

10420

Middle Eastern (MID)

AF:

0.640

AC:

187

AN:

292

European-Non Finnish (NFE)

AF:

0.691

AC:

46042

AN:

66612

Other (OTH)

AF:

0.678

AC:

1393

AN:

2054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.552

Heterozygous variant carriers

1448

2897

4345

5794

7242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<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:

0.671

Hom.:

3090

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.3

(source)

DANN

Benign

0.50

PhyloP100

-3.0

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