rs2744117

Variant summary

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

The NM_001163558.3(PRL):​c.-98+150C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 152,140 control chromosomes in the GnomAD database, including 649 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 0.076 ( 649 hom., cov: 32)

Consequence

PRL
NM_001163558.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.319
Variant links:
Genes affected
PRL (HGNC:9445): (prolactin) This gene encodes the anterior pituitary hormone prolactin. This secreted hormone is a growth regulator for many tissues, including cells of the immune system. It may also play a role in cell survival by suppressing apoptosis, and it is essential for lactation. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Aug 2011]
CASC15 (HGNC:28245): (cancer susceptibility 15) This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [provided by RefSeq, Dec 2017]

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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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PRLNM_001163558.3 linkuse as main transcriptc.-98+150C>A intron_variant
PRLXM_011514753.3 linkuse as main transcriptc.-98+150C>A intron_variant
PRLXM_011514754.3 linkuse as main transcriptc.-111+150C>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PRLENST00000651245.1 linkuse as main transcriptc.-98+150C>A intron_variant
PRLENST00000651757.1 linkuse as main transcriptc.-98+150C>A intron_variant
CASC15ENST00000561912.3 linkuse as main transcriptn.569+11622G>T intron_variant, non_coding_transcript_variant 5
CASC15ENST00000651569.1 linkuse as main transcriptn.505+11622G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0763
AC:
11596
AN:
152022
Hom.:
647
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0284
Gnomad AMI
AF:
0.123
Gnomad AMR
AF:
0.145
Gnomad ASJ
AF:
0.0643
Gnomad EAS
AF:
0.231
Gnomad SAS
AF:
0.119
Gnomad FIN
AF:
0.0412
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0803
Gnomad OTH
AF:
0.0828
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0762
AC:
11598
AN:
152140
Hom.:
649
Cov.:
32
AF XY:
0.0782
AC XY:
5816
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.0283
Gnomad4 AMR
AF:
0.145
Gnomad4 ASJ
AF:
0.0643
Gnomad4 EAS
AF:
0.231
Gnomad4 SAS
AF:
0.118
Gnomad4 FIN
AF:
0.0412
Gnomad4 NFE
AF:
0.0803
Gnomad4 OTH
AF:
0.0843
Alfa
AF:
0.0838
Hom.:
197
Bravo
AF:
0.0809
Asia WGS
AF:
0.189
AC:
656
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
2.5
DANN
Benign
0.28

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: rs2744117; hg19: chr6-22302839; API