dbSNP rs1476587: ENSG00000307585:n.364+6886A>G (chr7-87067398-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000827229.1(ENSG00000307585):n.364+6886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,136 control chromosomes in the GnomAD database, including 1,375 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 0.13 ( 1375 hom., cov: 32)

Consequence

ENSG00000307585
ENST00000827229.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.662

Publications

8 publications found

Variant links:

Genes affected

ENSG00000307585 (HGNC:):

ENSG00000307585 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000307585	ENST00000827229.1 link	n.364+6886A>G	intron_variant	Intron 2 of 3
ENSG00000307585	ENST00000827230.1 link	n.360+6886A>G	intron_variant	Intron 2 of 4
ENSG00000307585	ENST00000827231.1 link	n.359+6886A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19412

AN:

152018

Hom.:

1372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.128

AC:

19448

AN:

152136

Hom.:

1375

Cov.:

AF XY:

0.130

AC XY:

9677

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.119

AC:

4955

AN:

41522

American (AMR)

AF:

0.142

AC:

2166

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

347

AN:

3468

East Asian (EAS)

AF:

0.305

AC:

1580

AN:

5178

South Asian (SAS)

AF:

0.155

AC:

745

AN:

4816

European-Finnish (FIN)

AF:

0.158

AC:

1673

AN:

10590

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7620

AN:

67956

Other (OTH)

AF:

0.112

AC:

237

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

870

1740

2609

3479

4349

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.123

Hom.:

3375

Bravo

AF:

0.128

Asia WGS

AF:

0.253

AC:

874

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

8.8

(source)

DANN

Benign

0.92

PhyloP100

0.66

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