Menu
GeneBe

rs7760698

Variant summary

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

The NR_152835.1(PSORS1C3):n.292+3578A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0427 in 152,320 control chromosomes in the GnomAD database, including 220 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 0.043 ( 220 hom., cov: 31)

Consequence

PSORS1C3
NR_152835.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PSORS1C3NR_152835.1 linkuse as main transcriptn.292+3578A>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0428
AC:
6510
AN:
152202
Hom.:
219
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0161
Gnomad AMI
AF:
0.0285
Gnomad AMR
AF:
0.0590
Gnomad ASJ
AF:
0.216
Gnomad EAS
AF:
0.0133
Gnomad SAS
AF:
0.0876
Gnomad FIN
AF:
0.0392
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0457
Gnomad OTH
AF:
0.0561
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0427
AC:
6507
AN:
152320
Hom.:
220
Cov.:
31
AF XY:
0.0440
AC XY:
3276
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0160
Gnomad4 AMR
AF:
0.0588
Gnomad4 ASJ
AF:
0.216
Gnomad4 EAS
AF:
0.0135
Gnomad4 SAS
AF:
0.0870
Gnomad4 FIN
AF:
0.0392
Gnomad4 NFE
AF:
0.0457
Gnomad4 OTH
AF:
0.0570
Alfa
AF:
0.0497
Hom.:
28
Bravo
AF:
0.0429
Asia WGS
AF:
0.0550
AC:
191
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
4.0
Dann
Benign
0.45

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: rs7760698; hg19: chr6-31150225; API