rs1455638

Positions:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.60 ( 8136 hom., cov: 6)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.799
Variant links:

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ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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:
0.00
AC:
26327
AN:
44164
Hom.:
8138
Cov.:
6
FAILED QC
Gnomad AFR
AF:
0.797
Gnomad AMI
AF:
0.518
Gnomad AMR
AF:
0.557
Gnomad ASJ
AF:
0.589
Gnomad EAS
AF:
0.581
Gnomad SAS
AF:
0.493
Gnomad FIN
AF:
0.661
Gnomad MID
AF:
0.648
Gnomad NFE
AF:
0.555
Gnomad OTH
AF:
0.585
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.596
AC:
26310
AN:
44124
Hom.:
8136
Cov.:
6
AF XY:
0.601
AC XY:
11722
AN XY:
19516
show subpopulations
Gnomad4 AFR
AF:
0.797
Gnomad4 AMR
AF:
0.559
Gnomad4 ASJ
AF:
0.589
Gnomad4 EAS
AF:
0.582
Gnomad4 SAS
AF:
0.489
Gnomad4 FIN
AF:
0.661
Gnomad4 NFE
AF:
0.555
Gnomad4 OTH
AF:
0.580
Alfa
AF:
0.651
Hom.:
2850

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.5

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: rs1455638; hg19: chr8-2260986; API