dbSNP rs10496382: LOC105373523:n.541+4864G>A (chr2-104120276-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The XR_923127.1(LOC105373523):n.541+4864G>A variant causes a intron change. The variant allele was found at a frequency of 0.0683 in 152,152 control chromosomes in the GnomAD database, including 386 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 0.068 ( 386 hom., cov: 32)

Consequence

LOC105373523
XR_923127.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.60

Publications

0 publications found

Variant links:

Genes affected

LOC105373523 (HGNC:):

LOC105373523 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.19).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373523	XR_923127.1 link	n.541+4864G>A		intron_variant	Intron 5 of 6
LOC105373523	XR_923128.1 link	n.537+4864G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0683

AC:

10380

AN:

152034

Hom.:

385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0878

Gnomad AMI

AF:

0.0505

Gnomad AMR

AF:

0.0586

Gnomad ASJ

AF:

0.0838

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0757

Gnomad FIN

AF:

0.0970

Gnomad MID

AF:

0.0701

Gnomad NFE

AF:

0.0579

Gnomad OTH

AF:

0.0747

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

GnomAD4 genome

AF:

0.0683

AC:

10388

AN:

152152

Hom.:

386

Cov.:

AF XY:

0.0688

AC XY:

5115

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0878

AC:

3647

AN:

41514

American (AMR)

AF:

0.0583

AC:

891

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0838

AC:

291

AN:

3472

East Asian (EAS)

AF:

0.00116

AC:

AN:

5170

South Asian (SAS)

AF:

0.0762

AC:

367

AN:

4818

European-Finnish (FIN)

AF:

0.0970

AC:

1027

AN:

10584

Middle Eastern (MID)

AF:

0.0685

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0579

AC:

3937

AN:

68002

Other (OTH)

AF:

0.0739

AC:

156

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

512

1025

1537

2050

2562

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0622

Hom.:

405

Bravo

AF:

0.0654

Asia WGS

AF:

0.0380

AC:

133

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.19

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

5.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs10496382

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