13-30856349-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 0.681 in 152,028 control chromosomes in the GnomAD database, including 35,659 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 0.68 ( 35659 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.271
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.792 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:
0.680
AC:
103372
AN:
151910
Hom.:
35625
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.580
Gnomad AMI
AF:
0.815
Gnomad AMR
AF:
0.714
Gnomad ASJ
AF:
0.670
Gnomad EAS
AF:
0.716
Gnomad SAS
AF:
0.812
Gnomad FIN
AF:
0.740
Gnomad MID
AF:
0.614
Gnomad NFE
AF:
0.712
Gnomad OTH
AF:
0.663
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.681
AC:
103463
AN:
152028
Hom.:
35659
Cov.:
31
AF XY:
0.687
AC XY:
51058
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.580
Gnomad4 AMR
AF:
0.714
Gnomad4 ASJ
AF:
0.670
Gnomad4 EAS
AF:
0.716
Gnomad4 SAS
AF:
0.813
Gnomad4 FIN
AF:
0.740
Gnomad4 NFE
AF:
0.712
Gnomad4 OTH
AF:
0.666
Alfa
AF:
0.709
Hom.:
19183
Bravo
AF:
0.668
Asia WGS
AF:
0.756
AC:
2627
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.8
DANN
Benign
0.72

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: rs1831549; hg19: chr13-31430486; COSMIC: COSV69345991; API