dbSNP rs12229182: LOC124902904:n.27110699T>C (chr12-27110699-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 variant allele was found at a frequency of 0.0732 in 152,194 control chromosomes in the GnomAD database, including 671 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 0.073 ( 671 hom., cov: 32)

Consequence

LOC124902904
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.609

Publications

3 publications found

Variant links:

Genes affected

LOC124902904 (HGNC:):

LOC124902904 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 (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902904		n.27110699T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256226	ENST00000538920.1 link	n.244-5441A>G		intron_variant	Intron 1 of 1	5
ENSG00000256226	ENST00000824827.1 link	n.281-5441A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0732

AC:

11131

AN:

152076

Hom.:

668

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0179

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.0242

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.0880

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0675

Gnomad OTH

AF:

0.0722

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

GnomAD4 genome

AF:

0.0732

AC:

11144

AN:

152194

Hom.:

671

Cov.:

AF XY:

0.0769

AC XY:

5722

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0178

AC:

741

AN:

41548

American (AMR)

AF:

0.200

AC:

3056

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0242

AC:

AN:

3466

East Asian (EAS)

AF:

0.163

AC:

846

AN:

5180

South Asian (SAS)

AF:

0.125

AC:

604

AN:

4816

European-Finnish (FIN)

AF:

0.0880

AC:

932

AN:

10590

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0675

AC:

4589

AN:

67988

Other (OTH)

AF:

0.0752

AC:

159

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

508

1016

1525

2033

2541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0702

Hom.:

515

Bravo

AF:

0.0809

Asia WGS

AF:

0.148

AC:

515

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

1.6

(source)

DANN

Benign

0.59

PhyloP100

-0.61

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs12229182

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