rs8050940

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 0.092 in 152,156 control chromosomes in the GnomAD database, including 1,604 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 0.092 ( 1604 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216
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=-0.78).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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:
0.0915
AC:
13919
AN:
152038
Hom.:
1584
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.274
Gnomad AMI
AF:
0.0504
Gnomad AMR
AF:
0.0387
Gnomad ASJ
AF:
0.0112
Gnomad EAS
AF:
0.0400
Gnomad SAS
AF:
0.0360
Gnomad FIN
AF:
0.0181
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0178
Gnomad OTH
AF:
0.0674
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0920
AC:
13991
AN:
152156
Hom.:
1604
Cov.:
32
AF XY:
0.0900
AC XY:
6696
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.275
Gnomad4 AMR
AF:
0.0386
Gnomad4 ASJ
AF:
0.0112
Gnomad4 EAS
AF:
0.0403
Gnomad4 SAS
AF:
0.0354
Gnomad4 FIN
AF:
0.0181
Gnomad4 NFE
AF:
0.0178
Gnomad4 OTH
AF:
0.0662
Alfa
AF:
0.0307
Hom.:
394
Bravo
AF:
0.102
Asia WGS
AF:
0.0580
AC:
202
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
0.46
DANN
Benign
0.72

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: rs8050940; hg19: chr16-62100211; API