dbSNP rs9896573: ENSG00000298578:n.426-4470A>G (chr17-70142903-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 ENST00000756635.1(ENSG00000298578):n.426-4470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,290 control chromosomes in the GnomAD database, including 951 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 0.11 ( 951 hom., cov: 32)

Consequence

ENSG00000298578
ENST00000756635.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0620

Publications

4 publications found

Variant links:

Genes affected

ENSG00000298578 (HGNC:):

ENSG00000298578 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 (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371882	XR_934953.3 link	n.425-4470A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298578	ENST00000756635.1 link	n.426-4470A>G	intron_variant	Intron 3 of 3
ENSG00000298578	ENST00000756636.1 link	n.414-3439A>G	intron_variant	Intron 3 of 4
ENSG00000298578	ENST00000756637.1 link	n.504-3439A>G	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17261

AN:

152172

Hom.:

949

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0860

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.0958

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.120

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

GnomAD4 genome

AF:

0.113

AC:

17275

AN:

152290

Hom.:

951

Cov.:

AF XY:

0.114

AC XY:

8505

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.0859

AC:

3568

AN:

41552

American (AMR)

AF:

0.175

AC:

2686

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

443

AN:

3468

East Asian (EAS)

AF:

0.101

AC:

523

AN:

5182

South Asian (SAS)

AF:

0.169

AC:

816

AN:

4830

European-Finnish (FIN)

AF:

0.0958

AC:

1017

AN:

10614

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7845

AN:

68020

Other (OTH)

AF:

0.118

AC:

249

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

801

1601

2402

3202

4003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.0773

Hom.:

111

Bravo

AF:

0.118

Asia WGS

AF:

0.121

AC:

419

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

0.34

(source)

DANN

Benign

0.71

PhyloP100

-0.062

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