rs11258317

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 0.32 in 152,044 control chromosomes in the GnomAD database, including 8,354 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 0.32 ( 8354 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.195
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 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:
0.320
AC:
48632
AN:
151926
Hom.:
8352
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.244
Gnomad AMI
AF:
0.400
Gnomad AMR
AF:
0.284
Gnomad ASJ
AF:
0.306
Gnomad EAS
AF:
0.0292
Gnomad SAS
AF:
0.271
Gnomad FIN
AF:
0.426
Gnomad MID
AF:
0.345
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.329
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.320
AC:
48662
AN:
152044
Hom.:
8354
Cov.:
32
AF XY:
0.320
AC XY:
23766
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.244
Gnomad4 AMR
AF:
0.283
Gnomad4 ASJ
AF:
0.306
Gnomad4 EAS
AF:
0.0293
Gnomad4 SAS
AF:
0.273
Gnomad4 FIN
AF:
0.426
Gnomad4 NFE
AF:
0.383
Gnomad4 OTH
AF:
0.326
Alfa
AF:
0.357
Hom.:
9551
Bravo
AF:
0.304
Asia WGS
AF:
0.148
AC:
518
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.70
DANN
Benign
0.33

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: rs11258317; hg19: chr10-6407737; API