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GeneBe

rs3102078

Variant summary

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

The NR_125431.1(LOC101929128):n.287+3629C>A 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 0.585 in 151,920 control chromosomes in the GnomAD database, including 26,486 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 0.58 ( 26486 hom., cov: 31)

Consequence

LOC101929128
NR_125431.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.73
Variant links:
Genes affected
PPP1R3B-DT (HGNC:56150): (PPP1R3B divergent transcript)

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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC101929128NR_125431.1 linkuse as main transcriptn.287+3629C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PPP1R3B-DTENST00000512942.8 linkuse as main transcriptn.268+3618C>A intron_variant, non_coding_transcript_variant 1
PPP1R3B-DTENST00000417333.7 linkuse as main transcriptn.239+3629C>A intron_variant, non_coding_transcript_variant 5
PPP1R3B-DTENST00000523747.1 linkuse as main transcriptn.83-743C>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.585
AC:
88770
AN:
151802
Hom.:
26474
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.579
Gnomad AMI
AF:
0.662
Gnomad AMR
AF:
0.591
Gnomad ASJ
AF:
0.761
Gnomad EAS
AF:
0.287
Gnomad SAS
AF:
0.403
Gnomad FIN
AF:
0.462
Gnomad MID
AF:
0.728
Gnomad NFE
AF:
0.630
Gnomad OTH
AF:
0.622
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.585
AC:
88818
AN:
151920
Hom.:
26486
Cov.:
31
AF XY:
0.572
AC XY:
42503
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.578
Gnomad4 AMR
AF:
0.592
Gnomad4 ASJ
AF:
0.761
Gnomad4 EAS
AF:
0.287
Gnomad4 SAS
AF:
0.403
Gnomad4 FIN
AF:
0.462
Gnomad4 NFE
AF:
0.630
Gnomad4 OTH
AF:
0.617
Alfa
AF:
0.607
Hom.:
3902
Bravo
AF:
0.596
Asia WGS
AF:
0.361
AC:
1253
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.054
Dann
Benign
0.61

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: rs3102078; hg19: chr8-9050725; API