rs16931419

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 0.223 in 152,144 control chromosomes in the GnomAD database, including 5,107 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 0.22 ( 5107 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.190
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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:
0.223
AC:
33972
AN:
152026
Hom.:
5104
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.428
Gnomad AMI
AF:
0.373
Gnomad AMR
AF:
0.144
Gnomad ASJ
AF:
0.174
Gnomad EAS
AF:
0.194
Gnomad SAS
AF:
0.173
Gnomad FIN
AF:
0.108
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.142
Gnomad OTH
AF:
0.212
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.223
AC:
34001
AN:
152144
Hom.:
5107
Cov.:
32
AF XY:
0.219
AC XY:
16322
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.427
Gnomad4 AMR
AF:
0.144
Gnomad4 ASJ
AF:
0.174
Gnomad4 EAS
AF:
0.194
Gnomad4 SAS
AF:
0.172
Gnomad4 FIN
AF:
0.108
Gnomad4 NFE
AF:
0.142
Gnomad4 OTH
AF:
0.214
Alfa
AF:
0.150
Hom.:
2964
Bravo
AF:
0.236
Asia WGS
AF:
0.191
AC:
664
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.48
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: rs16931419; hg19: chr9-132497550; API