10-13141934-G-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 0.338 in 151,490 control chromosomes in the GnomAD database, including 8,935 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 0.34 ( 8935 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34
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=-1.02).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.338
AC:
51093
AN:
151374
Hom.:
8925
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.407
Gnomad AMI
AF:
0.258
Gnomad AMR
AF:
0.433
Gnomad ASJ
AF:
0.333
Gnomad EAS
AF:
0.341
Gnomad SAS
AF:
0.302
Gnomad FIN
AF:
0.227
Gnomad MID
AF:
0.364
Gnomad NFE
AF:
0.293
Gnomad OTH
AF:
0.371
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.338
AC:
51139
AN:
151490
Hom.:
8935
Cov.:
31
AF XY:
0.337
AC XY:
24914
AN XY:
73992
show subpopulations
Gnomad4 AFR
AF:
0.408
Gnomad4 AMR
AF:
0.433
Gnomad4 ASJ
AF:
0.333
Gnomad4 EAS
AF:
0.340
Gnomad4 SAS
AF:
0.300
Gnomad4 FIN
AF:
0.227
Gnomad4 NFE
AF:
0.293
Gnomad4 OTH
AF:
0.369
Alfa
AF:
0.241
Hom.:
840
Bravo
AF:
0.361
Asia WGS
AF:
0.335
AC:
1166
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.4
DANN
Benign
0.35

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: rs2095387; hg19: chr10-13183934; API