15-96475503-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 0.112 in 152,144 control chromosomes in the GnomAD database, including 1,245 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 0.11 ( 1245 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133
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=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.112
AC:
17040
AN:
152028
Hom.:
1247
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0290
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.0908
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.0211
Gnomad SAS
AF:
0.117
Gnomad FIN
AF:
0.144
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.166
Gnomad OTH
AF:
0.120
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
17029
AN:
152144
Hom.:
1245
Cov.:
31
AF XY:
0.110
AC XY:
8159
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.0289
Gnomad4 AMR
AF:
0.0906
Gnomad4 ASJ
AF:
0.154
Gnomad4 EAS
AF:
0.0211
Gnomad4 SAS
AF:
0.117
Gnomad4 FIN
AF:
0.144
Gnomad4 NFE
AF:
0.166
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.133
Hom.:
187
Bravo
AF:
0.104
Asia WGS
AF:
0.0970
AC:
338
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.3
DANN
Benign
0.45

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: rs113154706; hg19: chr15-97018733; API