dbSNP rs10505417: ENSG00000254303:n.160+26494G>A (chr8-122100531-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000523792.1(ENSG00000254303):n.160+26494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0157 in 152,126 control chromosomes in the GnomAD database, including 64 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 0.016 ( 64 hom., cov: 32)

Consequence

ENSG00000254303
ENST00000523792.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.947

Publications

2 publications found

Variant links:

Genes affected

ENSG00000254303 (HGNC:):

ENSG00000254303 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0664 is higher than 0.05.

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
ENSG00000254303	ENST00000523792.1 link	n.160+26494G>A		intron_variant	Intron 1 of 2	1
ENSG00000254303	ENST00000770642.1 link	n.122+26494G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0156

AC:

2378

AN:

152008

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00490

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0696

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.0365

Gnomad SAS

AF:

0.00623

Gnomad FIN

AF:

0.00340

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0120

Gnomad OTH

AF:

0.0187

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

GnomAD4 genome

AF:

0.0157

AC:

2384

AN:

152126

Hom.:

Cov.:

AF XY:

0.0160

AC XY:

1190

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.00489

AC:

203

AN:

41520

American (AMR)

AF:

0.0699

AC:

1066

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.000865

AC:

AN:

3470

East Asian (EAS)

AF:

0.0366

AC:

189

AN:

5168

South Asian (SAS)

AF:

0.00644

AC:

AN:

4810

European-Finnish (FIN)

AF:

0.00340

AC:

AN:

10584

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0120

AC:

818

AN:

67998

Other (OTH)

AF:

0.0180

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

104

209

313

418

522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<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:

0.0172

Hom.:

Bravo

AF:

0.0244

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.84

(source)

DANN

Benign

0.80

PhyloP100

-0.95

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