rs1355459

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 0.314 in 151,784 control chromosomes in the GnomAD database, including 7,816 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 0.31 ( 7816 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.547
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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 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:
0.314
AC:
47688
AN:
151668
Hom.:
7807
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.361
Gnomad AMI
AF:
0.235
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.310
Gnomad EAS
AF:
0.0788
Gnomad SAS
AF:
0.375
Gnomad FIN
AF:
0.324
Gnomad MID
AF:
0.285
Gnomad NFE
AF:
0.318
Gnomad OTH
AF:
0.323
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.314
AC:
47731
AN:
151784
Hom.:
7816
Cov.:
32
AF XY:
0.314
AC XY:
23255
AN XY:
74154
show subpopulations
Gnomad4 AFR
AF:
0.361
Gnomad4 AMR
AF:
0.233
Gnomad4 ASJ
AF:
0.310
Gnomad4 EAS
AF:
0.0789
Gnomad4 SAS
AF:
0.376
Gnomad4 FIN
AF:
0.324
Gnomad4 NFE
AF:
0.318
Gnomad4 OTH
AF:
0.323
Alfa
AF:
0.318
Hom.:
984
Bravo
AF:
0.305
Asia WGS
AF:
0.240
AC:
827
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.21
DANN
Benign
0.20

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: rs1355459; hg19: chr6-23871700; COSMIC: COSV69193792; API