rs7111562

Positions:

• chr11-19030325-T-C

Variant summary

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

The ENST00000532323.1(MRGPRX9P):​n.114A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,104 control chromosomes in the GnomAD database, including 1,650 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 0.15 (1649 hom., cov: 32)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: MRGPRX9P ENST00000532323.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

MRGPRX9P (HGNC:54333): (MAS related GPR family member X9, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRGPRX9P	ENST00000532323.1	n.114A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22200 AN: 151908 Hom.: 1650 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.137

GnomAD4 exome AF: 0.115 AC: 9 AN: 78 Hom.: 1 Cov.: 0 AF XY: 0.103 AC XY: 7 AN XY: 68

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.117

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.146 AC: 22220 AN: 152026 Hom.: 1649 Cov.: 32 AF XY: 0.145 AC XY: 10807 AN XY: 74284

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.136

Alfa AF: 0.138 Hom.: 2531

Bravo AF: 0.146

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7111562; hg19: chr11-19051872;