rs10484596

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 0.0635 in 152,260 control chromosomes in the GnomAD database, including 670 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 0.063 ( 670 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 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:
0.0633
AC:
9627
AN:
152142
Hom.:
665
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.173
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0304
Gnomad ASJ
AF:
0.0216
Gnomad EAS
AF:
0.000384
Gnomad SAS
AF:
0.0416
Gnomad FIN
AF:
0.0182
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0205
Gnomad OTH
AF:
0.0611
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0635
AC:
9662
AN:
152260
Hom.:
670
Cov.:
32
AF XY:
0.0618
AC XY:
4604
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.173
Gnomad4 AMR
AF:
0.0304
Gnomad4 ASJ
AF:
0.0216
Gnomad4 EAS
AF:
0.000385
Gnomad4 SAS
AF:
0.0413
Gnomad4 FIN
AF:
0.0182
Gnomad4 NFE
AF:
0.0205
Gnomad4 OTH
AF:
0.0605
Alfa
AF:
0.0473
Hom.:
92
Bravo
AF:
0.0700
Asia WGS
AF:
0.0240
AC:
86
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.9
DANN
Benign
0.59

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: rs10484596; hg19: chr6-137731944; API