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rs599839

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The 1-109279544-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151912 control chromosomes in the gnomAD Genomes database, including 34921 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 0.64 ( 34921 hom., cov: 32)

Consequence

PSRC1
NM_001032291.3 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.902

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PSRC1NM_001032291.3 linkuse as main transcript downstream_gene_variant ENST00000369909.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PSRC1ENST00000369909.7 linkuse as main transcript downstream_gene_variant 1 NM_001032291.3 P2Q6PGN9-2

Frequencies

GnomAD3 genomes
AF:
0.638
AC:
96922
AN:
151912
Hom.:
34921
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.277
Gnomad AMI
AF:
0.658
Gnomad AMR
AF:
0.737
Gnomad ASJ
AF:
0.828
Gnomad EAS
AF:
0.922
Gnomad SAS
AF:
0.746
Gnomad FIN
AF:
0.775
Gnomad MID
AF:
0.850
Gnomad NFE
AF:
0.772
Gnomad OTH
AF:
0.685
GnomAD4 exome
AF:
0.810
AC:
209
AN:
258
Hom.:
83
AF XY:
0.808
AC XY:
118
AN XY:
146
show subpopulations
Gnomad4 AMR exome
AF:
0.500
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
0.809
Gnomad4 NFE exome
AF:
0.833
Gnomad4 OTH exome
AF:
1.00
Alfa
AF:
0.754
Hom.:
60561
Bravo
AF:
0.618
Asia WGS
AF:
0.790
AC:
2749
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.27
Dann
Benign
0.81

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: rs599839; hg19: chr1-109822166; API