rs387504

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 0.279 in 151,686 control chromosomes in the GnomAD database, including 6,626 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 0.28 ( 6626 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34
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=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 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:
0.279
AC:
42345
AN:
151568
Hom.:
6618
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.126
Gnomad AMI
AF:
0.405
Gnomad AMR
AF:
0.382
Gnomad ASJ
AF:
0.380
Gnomad EAS
AF:
0.332
Gnomad SAS
AF:
0.262
Gnomad FIN
AF:
0.306
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.334
Gnomad OTH
AF:
0.320
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.279
AC:
42360
AN:
151686
Hom.:
6626
Cov.:
32
AF XY:
0.282
AC XY:
20888
AN XY:
74108
show subpopulations
Gnomad4 AFR
AF:
0.126
Gnomad4 AMR
AF:
0.383
Gnomad4 ASJ
AF:
0.380
Gnomad4 EAS
AF:
0.333
Gnomad4 SAS
AF:
0.262
Gnomad4 FIN
AF:
0.306
Gnomad4 NFE
AF:
0.334
Gnomad4 OTH
AF:
0.318
Alfa
AF:
0.307
Hom.:
941
Bravo
AF:
0.280
Asia WGS
AF:
0.268
AC:
930
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.9
DANN
Benign
0.26

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: rs387504; hg19: chr19-44445988; API