rs16878312

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 0.255 in 151,870 control chromosomes in the GnomAD database, including 5,163 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 0.25 ( 5163 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75
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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 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:
0.255
AC:
38632
AN:
151750
Hom.:
5160
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.315
Gnomad AMR
AF:
0.191
Gnomad ASJ
AF:
0.281
Gnomad EAS
AF:
0.0601
Gnomad SAS
AF:
0.328
Gnomad FIN
AF:
0.277
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.303
Gnomad OTH
AF:
0.251
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.255
AC:
38654
AN:
151870
Hom.:
5163
Cov.:
32
AF XY:
0.253
AC XY:
18761
AN XY:
74190
show subpopulations
Gnomad4 AFR
AF:
0.205
Gnomad4 AMR
AF:
0.191
Gnomad4 ASJ
AF:
0.281
Gnomad4 EAS
AF:
0.0604
Gnomad4 SAS
AF:
0.327
Gnomad4 FIN
AF:
0.277
Gnomad4 NFE
AF:
0.303
Gnomad4 OTH
AF:
0.247
Alfa
AF:
0.277
Hom.:
5722
Bravo
AF:
0.239
Asia WGS
AF:
0.189
AC:
656
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.14
DANN
Benign
0.31

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: rs16878312; hg19: chr5-71705384; API