dbSNP rs12256364: LOC105378313:n.483+9053C>T (chr10-57335928-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 XR_001747453.1(LOC105378313):n.483+9053C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,148 control chromosomes in the GnomAD database, including 3,709 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 0.16 ( 3709 hom., cov: 33)

Consequence

LOC105378313
XR_001747453.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.733

Publications

4 publications found

Variant links:

Genes affected

LOC105378313 (HGNC:):

LOC105378313 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378313	XR_001747453.1 link	n.483+9053C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308896	ENST00000837137.1 link	n.*51C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23930

AN:

152026

Hom.:

3698

Cov.:

show subpopulations

Gnomad AFR

AF:

0.395

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.0452

Gnomad EAS

AF:

0.0936

Gnomad SAS

AF:

0.0857

Gnomad FIN

AF:

0.0292

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0401

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.158

AC:

23995

AN:

152148

Hom.:

3709

Cov.:

AF XY:

0.158

AC XY:

11756

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.395

AC:

16398

AN:

41464

American (AMR)

AF:

0.207

AC:

3170

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0452

AC:

157

AN:

3470

East Asian (EAS)

AF:

0.0936

AC:

483

AN:

5158

South Asian (SAS)

AF:

0.0850

AC:

410

AN:

4826

European-Finnish (FIN)

AF:

0.0292

AC:

310

AN:

10608

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0401

AC:

2727

AN:

68024

Other (OTH)

AF:

0.136

AC:

287

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

876

1753

2629

3506

4382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.0595

Hom.:

396

Bravo

AF:

0.182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.20

(source)

DANN

Benign

0.65

PhyloP100

-0.73

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