rs1944423

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 0.629 in 151,996 control chromosomes in the GnomAD database, including 31,453 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 0.63 ( 31453 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.929
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=-0.82).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.717 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:
0.629
AC:
95532
AN:
151878
Hom.:
31445
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.453
Gnomad AMI
AF:
0.841
Gnomad AMR
AF:
0.726
Gnomad ASJ
AF:
0.711
Gnomad EAS
AF:
0.407
Gnomad SAS
AF:
0.448
Gnomad FIN
AF:
0.714
Gnomad MID
AF:
0.706
Gnomad NFE
AF:
0.722
Gnomad OTH
AF:
0.671
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.629
AC:
95583
AN:
151996
Hom.:
31453
Cov.:
31
AF XY:
0.629
AC XY:
46707
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.453
Gnomad4 AMR
AF:
0.726
Gnomad4 ASJ
AF:
0.711
Gnomad4 EAS
AF:
0.406
Gnomad4 SAS
AF:
0.450
Gnomad4 FIN
AF:
0.714
Gnomad4 NFE
AF:
0.722
Gnomad4 OTH
AF:
0.667
Alfa
AF:
0.646
Hom.:
4647
Bravo
AF:
0.630
Asia WGS
AF:
0.431
AC:
1502
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.58
DANN
Benign
0.49

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: rs1944423; hg19: chr18-60990518; API