rs1948368

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 0.533 in 151,772 control chromosomes in the GnomAD database, including 21,877 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 0.53 ( 21877 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.545
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 (AFR) allele frequency at 95% confidence interval = 0.603 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:
0.534
AC:
80910
AN:
151654
Hom.:
21868
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.609
Gnomad AMI
AF:
0.562
Gnomad AMR
AF:
0.497
Gnomad ASJ
AF:
0.572
Gnomad EAS
AF:
0.321
Gnomad SAS
AF:
0.491
Gnomad FIN
AF:
0.554
Gnomad MID
AF:
0.547
Gnomad NFE
AF:
0.510
Gnomad OTH
AF:
0.524
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.533
AC:
80956
AN:
151772
Hom.:
21877
Cov.:
32
AF XY:
0.532
AC XY:
39441
AN XY:
74170
show subpopulations
Gnomad4 AFR
AF:
0.609
Gnomad4 AMR
AF:
0.497
Gnomad4 ASJ
AF:
0.572
Gnomad4 EAS
AF:
0.321
Gnomad4 SAS
AF:
0.490
Gnomad4 FIN
AF:
0.554
Gnomad4 NFE
AF:
0.509
Gnomad4 OTH
AF:
0.523
Alfa
AF:
0.501
Hom.:
35735
Bravo
AF:
0.534
Asia WGS
AF:
0.435
AC:
1513
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.5
DANN
Benign
0.31

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: rs1948368; hg19: chr1-101938477; API