4-121370367-T-C

Position:

• chr4-121370367-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198179.3(QRFPR):​c.340+9941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 737,130 control chromosomes in the GnomAD database, including 214,556 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 0.77 (45601 hom., cov: 32)
  • Exomes 𝑓: 0.75 (168955 hom.)
• Consequence: QRFPR NM_198179.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

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]

KIAA1191P1 (HGNC:56785): (KIAA1191 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QRFPR	NM_198179.3	c.340+9941A>G		intron_variant		ENST00000394427.3
QRFPR	XM_017008693.3	c.340+9941A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QRFPR	ENST00000394427.3	c.340+9941A>G		intron_variant		1	NM_198179.3	P1
KIAA1191P1	ENST00000515076.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116695 AN: 152056 Hom.: 45562 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.770

GnomAD4 exome AF: 0.749 AC: 438414 AN: 584956 Hom.: 168955 Cov.: 2 AF XY: 0.749 AC XY: 239835 AN XY: 320182

Gnomad4 AFR exome AF: 0.786

Gnomad4 AMR exome AF: 0.588

Gnomad4 ASJ exome AF: 0.905

Gnomad4 EAS exome AF: 0.367

Gnomad4 SAS exome AF: 0.660

Gnomad4 FIN exome AF: 0.837

Gnomad4 NFE exome AF: 0.802

Gnomad4 OTH exome AF: 0.767

GnomAD4 genome AF: 0.767 AC: 116784 AN: 152174 Hom.: 45601 Cov.: 32 AF XY: 0.763 AC XY: 56741 AN XY: 74392

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.767

Alfa AF: 0.788 Hom.: 24468

Bravo AF: 0.756

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	2.3
DANN	Benign	0.65

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

Other links and lift over

dbSNP: rs2013332; hg19: chr4-122291522; COSMIC: COSV57678235; COSMIC: COSV57678235;