chr4-121359180-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_198179.3(QRFPR):​c.341-18570G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

QRFPR
NM_198179.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.874
Variant links:
Genes affected
QRFPR (HGNC:15565): (pyroglutamylated RFamide peptide receptor) Enables G protein-coupled receptor activity. Involved in G protein-coupled receptor signaling pathway. Predicted to be located in non-motile cilium. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
QRFPRNM_198179.3 linkuse as main transcriptc.341-18570G>A intron_variant ENST00000394427.3 NP_937822.2
QRFPRXM_017008693.3 linkuse as main transcriptc.341-18570G>A intron_variant XP_016864182.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
QRFPRENST00000394427.3 linkuse as main transcriptc.341-18570G>A intron_variant 1 NM_198179.3 ENSP00000377948 P1
QRFPRENST00000512235.1 linkuse as main transcriptn.753-18570G>A intron_variant, non_coding_transcript_variant 1
QRFPRENST00000334383.9 linkuse as main transcriptc.341-18570G>A intron_variant 2 ENSP00000335610
QRFPRENST00000507331.5 linkuse as main transcriptc.341-18570G>A intron_variant, NMD_transcript_variant 2 ENSP00000423369

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.50
DANN
Benign
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs10518388; hg19: chr4-122280335; API