rs5014418

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 0.117 in 152,042 control chromosomes in the GnomAD database, including 1,665 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 0.12 ( 1665 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0690
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 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:
0.117
AC:
17733
AN:
151924
Hom.:
1663
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.251
Gnomad AMI
AF:
0.0461
Gnomad AMR
AF:
0.130
Gnomad ASJ
AF:
0.0782
Gnomad EAS
AF:
0.00557
Gnomad SAS
AF:
0.0151
Gnomad FIN
AF:
0.00530
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0675
Gnomad OTH
AF:
0.150
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.117
AC:
17741
AN:
152042
Hom.:
1665
Cov.:
32
AF XY:
0.112
AC XY:
8336
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.250
Gnomad4 AMR
AF:
0.130
Gnomad4 ASJ
AF:
0.0782
Gnomad4 EAS
AF:
0.00539
Gnomad4 SAS
AF:
0.0151
Gnomad4 FIN
AF:
0.00530
Gnomad4 NFE
AF:
0.0676
Gnomad4 OTH
AF:
0.148
Alfa
AF:
0.0886
Hom.:
193
Bravo
AF:
0.138
Asia WGS
AF:
0.0210
AC:
72
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.2
DANN
Benign
0.71

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: rs5014418; hg19: chr6-32719381; API