chr13-60887877-T-C

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 0.89 in 151,824 control chromosomes in the GnomAD database, including 60,220 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 0.89 ( 60220 hom., cov: 30)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.73
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.60887877T>C intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC00378ENST00000658247.1 linkuse as main transcriptn.363+37351T>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.891
AC:
135097
AN:
151706
Hom.:
60180
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.857
Gnomad AMI
AF:
0.869
Gnomad AMR
AF:
0.930
Gnomad ASJ
AF:
0.935
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.901
Gnomad FIN
AF:
0.903
Gnomad MID
AF:
0.908
Gnomad NFE
AF:
0.889
Gnomad OTH
AF:
0.910
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.890
AC:
135195
AN:
151824
Hom.:
60220
Cov.:
30
AF XY:
0.892
AC XY:
66157
AN XY:
74206
show subpopulations
Gnomad4 AFR
AF:
0.857
Gnomad4 AMR
AF:
0.930
Gnomad4 ASJ
AF:
0.935
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.901
Gnomad4 FIN
AF:
0.903
Gnomad4 NFE
AF:
0.889
Gnomad4 OTH
AF:
0.912
Alfa
AF:
0.892
Hom.:
79269
Bravo
AF:
0.893
Asia WGS
AF:
0.951
AC:
3304
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.37
DANN
Benign
0.71

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: rs300310; hg19: chr13-61462011; API