1-47632734-A-G

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 0.458 in 151,942 control chromosomes in the GnomAD database, including 16,590 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 0.46 ( 16590 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347
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=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 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:
0.458
AC:
69514
AN:
151824
Hom.:
16584
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.325
Gnomad AMI
AF:
0.590
Gnomad AMR
AF:
0.568
Gnomad ASJ
AF:
0.585
Gnomad EAS
AF:
0.437
Gnomad SAS
AF:
0.484
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.506
Gnomad OTH
AF:
0.473
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.458
AC:
69560
AN:
151942
Hom.:
16590
Cov.:
31
AF XY:
0.460
AC XY:
34142
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.325
Gnomad4 AMR
AF:
0.568
Gnomad4 ASJ
AF:
0.585
Gnomad4 EAS
AF:
0.438
Gnomad4 SAS
AF:
0.483
Gnomad4 FIN
AF:
0.447
Gnomad4 NFE
AF:
0.506
Gnomad4 OTH
AF:
0.470
Alfa
AF:
0.507
Hom.:
26221
Bravo
AF:
0.460
Asia WGS
AF:
0.467
AC:
1620
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
3.4
DANN
Benign
0.69

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: rs2506991; hg19: chr1-48098406; API