rs6482235

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 0.397 in 151,818 control chromosomes in the GnomAD database, including 14,121 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 0.40 ( 14121 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.86
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 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:
0.397
AC:
60163
AN:
151700
Hom.:
14079
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.653
Gnomad AMI
AF:
0.251
Gnomad AMR
AF:
0.264
Gnomad ASJ
AF:
0.359
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.369
Gnomad FIN
AF:
0.256
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.320
Gnomad OTH
AF:
0.395
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.397
AC:
60249
AN:
151818
Hom.:
14121
Cov.:
31
AF XY:
0.389
AC XY:
28862
AN XY:
74170
show subpopulations
Gnomad4 AFR
AF:
0.654
Gnomad4 AMR
AF:
0.264
Gnomad4 ASJ
AF:
0.359
Gnomad4 EAS
AF:
0.105
Gnomad4 SAS
AF:
0.368
Gnomad4 FIN
AF:
0.256
Gnomad4 NFE
AF:
0.320
Gnomad4 OTH
AF:
0.395
Alfa
AF:
0.331
Hom.:
12551
Bravo
AF:
0.406
Asia WGS
AF:
0.272
AC:
948
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.63
DANN
Benign
0.70

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: rs6482235; hg19: chr10-23022966; API