dbSNP rs10485711: ENSG00000232271:n.81+13806T>C (chr20-7083500-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 ENST00000425900.1(ENSG00000232271):n.81+13806T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,914 control chromosomes in the GnomAD database, including 5,344 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 0.22 ( 5344 hom., cov: 32)

Consequence

ENSG00000232271
ENST00000425900.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104

Publications

0 publications found

Variant links:

Genes affected

ENSG00000232271 (HGNC:):

ENSG00000232271 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 (AFR) allele frequency at 95% confidence interval = 0.444 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
ENSG00000232271	ENST00000425900.1 link	n.81+13806T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33541

AN:

151796

Hom.:

5317

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.217

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

GnomAD4 genome

AF:

0.221

AC:

33620

AN:

151914

Hom.:

5344

Cov.:

AF XY:

0.221

AC XY:

16412

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.449

AC:

18612

AN:

41422

American (AMR)

AF:

0.243

AC:

3699

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.109

AC:

377

AN:

3468

East Asian (EAS)

AF:

0.212

AC:

1092

AN:

5142

South Asian (SAS)

AF:

0.104

AC:

500

AN:

4826

European-Finnish (FIN)

AF:

0.103

AC:

1097

AN:

10604

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.113

AC:

7705

AN:

67900

Other (OTH)

AF:

0.217

AC:

458

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1185

2370

3556

4741

5926

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<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:

0.161

Hom.:

1143

Bravo

AF:

0.245

Asia WGS

AF:

0.203

AC:

703

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

2.4

(source)

DANN

Benign

0.49

PhyloP100

-0.10

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