13-37561466-G-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 0.708 in 152,106 control chromosomes in the GnomAD database, including 38,508 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 0.71 ( 38508 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74
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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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:
0.708
AC:
107549
AN:
151990
Hom.:
38472
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.791
Gnomad AMI
AF:
0.728
Gnomad AMR
AF:
0.710
Gnomad ASJ
AF:
0.510
Gnomad EAS
AF:
0.836
Gnomad SAS
AF:
0.671
Gnomad FIN
AF:
0.754
Gnomad MID
AF:
0.709
Gnomad NFE
AF:
0.652
Gnomad OTH
AF:
0.692
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.708
AC:
107633
AN:
152106
Hom.:
38508
Cov.:
32
AF XY:
0.716
AC XY:
53268
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.791
Gnomad4 AMR
AF:
0.710
Gnomad4 ASJ
AF:
0.510
Gnomad4 EAS
AF:
0.836
Gnomad4 SAS
AF:
0.671
Gnomad4 FIN
AF:
0.754
Gnomad4 NFE
AF:
0.652
Gnomad4 OTH
AF:
0.690
Alfa
AF:
0.678
Hom.:
4381
Bravo
AF:
0.707
Asia WGS
AF:
0.740
AC:
2573
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.067
DANN
Benign
0.62

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: rs7994218; hg19: chr13-38135603; API