rs35951010

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 152,178 control chromosomes in the GnomAD database, including 1,359 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 ( 1359 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170
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=-0.55).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 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:
0.112
AC:
17025
AN:
152060
Hom.:
1358
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0256
Gnomad AMI
AF:
0.0504
Gnomad AMR
AF:
0.0788
Gnomad ASJ
AF:
0.105
Gnomad EAS
AF:
0.00269
Gnomad SAS
AF:
0.166
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.160
Gnomad OTH
AF:
0.121
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
17023
AN:
152178
Hom.:
1359
Cov.:
32
AF XY:
0.114
AC XY:
8509
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.0255
Gnomad4 AMR
AF:
0.0786
Gnomad4 ASJ
AF:
0.105
Gnomad4 EAS
AF:
0.00270
Gnomad4 SAS
AF:
0.166
Gnomad4 FIN
AF:
0.222
Gnomad4 NFE
AF:
0.160
Gnomad4 OTH
AF:
0.124
Alfa
AF:
0.0762
Hom.:
98
Bravo
AF:
0.0970
Asia WGS
AF:
0.105
AC:
365
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
8.2
DANN
Benign
0.78

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: rs35951010; hg19: chr6-88844731; COSMIC: COSV65673254; API