rs7111562

Variant names:

• chr11-19030325-T-C
• rs7111562
• ENST00000532323.1:n.114A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532323.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRGPRX9P	ENST00000532323.1	TSL:6	n.114A>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.117 AC: 7 AN: 60

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.173 AC: 7195 AN: 41474

American (AMR) AF: 0.113 AC: 1729 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3466

East Asian (EAS) AF: 0.203 AC: 1045 AN: 5160

South Asian (SAS) AF: 0.102 AC: 492 AN: 4812

European-Finnish (FIN) AF: 0.159 AC: 1677 AN: 10540

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9214 AN: 67982

Other (OTH) AF: 0.136 AC: 286 AN: 2106

Alfa AF: 0.140 Hom.: 6149

Bravo AF: 0.146

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.31
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7111562; hg19: chr11-19051872;