dbSNP rs10503985: ENSG00000253452:n.175+9620G>A (chr8-36156306-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000659919.1(ENSG00000253452):n.175+9620G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 152,292 control chromosomes in the GnomAD database, including 62 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 0.021 ( 62 hom., cov: 32)

Consequence

ENSG00000253452
ENST00000659919.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.211

Publications

0 publications found

Variant links:

Genes affected

ENSG00000253452 (HGNC:):

ENSG00000253452 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000253452	ENST00000659919.1 link	n.175+9620G>A	intron_variant	Intron 3 of 7
ENSG00000253452	ENST00000662333.1 link	n.224-20279G>A	intron_variant	Intron 2 of 3
ENSG00000253452	ENST00000723853.1 link	n.294-20279G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0209

AC:

3180

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0238

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00871

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.0631

Gnomad FIN

AF:

0.0387

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00988

Gnomad OTH

AF:

0.0205

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

GnomAD4 genome

AF:

0.0209

AC:

3189

AN:

152292

Hom.:

Cov.:

AF XY:

0.0234

AC XY:

1743

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.0238

AC:

989

AN:

41558

American (AMR)

AF:

0.00870

AC:

133

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00490

AC:

AN:

3470

East Asian (EAS)

AF:

0.117

AC:

606

AN:

5172

South Asian (SAS)

AF:

0.0636

AC:

307

AN:

4826

European-Finnish (FIN)

AF:

0.0387

AC:

411

AN:

10612

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00989

AC:

673

AN:

68038

Other (OTH)

AF:

0.0222

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

160

319

479

638

798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<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:

0.0152

Hom.:

Bravo

AF:

0.0188

Asia WGS

AF:

0.0970

AC:

337

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.0

(source)

DANN

Benign

0.58

PhyloP100

0.21

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