dbSNP rs9534578: ENSG00000297874:n.159-17883G>T (chr13-47269242-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000751481.1(ENSG00000297874):n.159-17883G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,952 control chromosomes in the GnomAD database, including 937 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 0.10 ( 937 hom., cov: 32)

Consequence

ENSG00000297874
ENST00000751481.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.613

Publications

2 publications found

Variant links:

Genes affected

ENSG00000297874 (HGNC:):

ENSG00000297874 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370195	XR_941947.1 link	n.521-939C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297874	ENST00000751481.1 link	n.159-17883G>T	intron_variant	Intron 1 of 3
ENSG00000297897	ENST00000751591.1 link	n.512-939C>A	intron_variant	Intron 2 of 2
ENSG00000297897	ENST00000751592.1 link	n.126-939C>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15833

AN:

151836

Hom.:

930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.0785

Gnomad ASJ

AF:

0.0686

Gnomad EAS

AF:

0.0235

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.0836

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0859

Gnomad OTH

AF:

0.0854

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

GnomAD4 genome

AF:

0.104

AC:

15870

AN:

151952

Hom.:

937

Cov.:

AF XY:

0.106

AC XY:

7873

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.150

AC:

6239

AN:

41462

American (AMR)

AF:

0.0784

AC:

1196

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0686

AC:

238

AN:

3468

East Asian (EAS)

AF:

0.0235

AC:

121

AN:

5146

South Asian (SAS)

AF:

0.198

AC:

948

AN:

4798

European-Finnish (FIN)

AF:

0.0836

AC:

883

AN:

10564

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0860

AC:

5841

AN:

67944

Other (OTH)

AF:

0.0845

AC:

178

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

723

1446

2168

2891

3614

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.0893

Hom.:

848

Bravo

AF:

0.104

Asia WGS

AF:

0.120

AC:

417

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.68

(source)

DANN

Benign

0.84

PhyloP100

-0.61

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