rs35916350

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 0.099 in 152,430 control chromosomes in the GnomAD database, including 925 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 0.099 ( 921 hom., cov: 33)
Exomes 𝑓: 0.16 ( 4 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.380
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=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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:
0.0989
AC:
15050
AN:
152124
Hom.:
919
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0386
Gnomad AMI
AF:
0.138
Gnomad AMR
AF:
0.0721
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.0777
Gnomad SAS
AF:
0.0403
Gnomad FIN
AF:
0.185
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.0994
GnomAD4 exome
AF:
0.160
AC:
30
AN:
188
Hom.:
4
AF XY:
0.169
AC XY:
24
AN XY:
142
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.250
Gnomad4 NFE exome
AF:
0.171
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0989
AC:
15053
AN:
152242
Hom.:
921
Cov.:
33
AF XY:
0.0979
AC XY:
7286
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0385
Gnomad4 AMR
AF:
0.0721
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.0771
Gnomad4 SAS
AF:
0.0403
Gnomad4 FIN
AF:
0.185
Gnomad4 NFE
AF:
0.133
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.107
Hom.:
102
Bravo
AF:
0.0901
Asia WGS
AF:
0.0710
AC:
245
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
5.4
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: rs35916350; hg19: chr5-174871354; API