rs243757

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 0.1 in 152,130 control chromosomes in the GnomAD database, including 1,269 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 0.10 ( 1269 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23
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 (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0999
AC:
15192
AN:
152012
Hom.:
1269
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.233
Gnomad AMI
AF:
0.0307
Gnomad AMR
AF:
0.0604
Gnomad ASJ
AF:
0.0510
Gnomad EAS
AF:
0.0143
Gnomad SAS
AF:
0.0147
Gnomad FIN
AF:
0.0256
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.0562
Gnomad OTH
AF:
0.0852
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.100
AC:
15208
AN:
152130
Hom.:
1269
Cov.:
32
AF XY:
0.0950
AC XY:
7064
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.232
Gnomad4 AMR
AF:
0.0602
Gnomad4 ASJ
AF:
0.0510
Gnomad4 EAS
AF:
0.0143
Gnomad4 SAS
AF:
0.0143
Gnomad4 FIN
AF:
0.0256
Gnomad4 NFE
AF:
0.0562
Gnomad4 OTH
AF:
0.0858
Alfa
AF:
0.0832
Hom.:
109
Bravo
AF:
0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.28
DANN
Benign
0.65

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: rs243757; hg19: chr6-54385981; API