chr12-101220625-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.237 in 152,050 control chromosomes in the GnomAD database, including 4,802 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 0.24 ( 4802 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 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

Frequencies

GnomAD3 genomes
AF:
0.237
AC:
36024
AN:
151934
Hom.:
4802
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.115
Gnomad AMI
AF:
0.330
Gnomad AMR
AF:
0.277
Gnomad ASJ
AF:
0.299
Gnomad EAS
AF:
0.333
Gnomad SAS
AF:
0.431
Gnomad FIN
AF:
0.227
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.278
Gnomad OTH
AF:
0.249
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.237
AC:
36033
AN:
152050
Hom.:
4802
Cov.:
32
AF XY:
0.238
AC XY:
17710
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.114
Gnomad4 AMR
AF:
0.277
Gnomad4 ASJ
AF:
0.299
Gnomad4 EAS
AF:
0.333
Gnomad4 SAS
AF:
0.431
Gnomad4 FIN
AF:
0.227
Gnomad4 NFE
AF:
0.278
Gnomad4 OTH
AF:
0.251
Alfa
AF:
0.271
Hom.:
4654
Bravo
AF:
0.231
Asia WGS
AF:
0.399
AC:
1387
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
2.1
DANN
Benign
0.44

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2062167; hg19: chr12-101614403; API