rs768911691

Variant names:

• chr3-142963282-C-A
• rs768911691
• NM_198504.4:c.55G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-142963282-C-A
• chr3-142963282-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198504.4(PAQR9):​c.55G>T​(p.Ala19Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000225 in 1,330,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A19T) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000023 (0 hom.)
• Consequence: PAQR9 NM_198504.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 0 publications found

Genes affected

PAQR9 (HGNC:30131): (progestin and adipoQ receptor family member 9) Predicted to enable signaling receptor activity. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

PAQR9-AS1 (HGNC:50861): (PAQR9 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.059765756).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198504.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR9	NM_198504.4	MANE Select	c.55G>T	p.Ala19Ser	missense	Exon 1 of 1	NP_940906.1	Q6ZVX9
	PAQR9	NM_001375300.1		c.55G>T	p.Ala19Ser	missense	Exon 2 of 4	NP_001362229.1
	PAQR9	NM_001375301.1		c.55G>T	p.Ala19Ser	missense	Exon 2 of 4	NP_001362230.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAQR9	ENST00000340634.6	TSL:6 MANE Select	c.55G>T	p.Ala19Ser	missense	Exon 1 of 1	ENSP00000341564.4	Q6ZVX9
	PAQR9	ENST00000900185.1		c.55G>T	p.Ala19Ser	missense	Exon 2 of 2	ENSP00000570244.1
	PAQR9	ENST00000900186.1		c.55G>T	p.Ala19Ser	missense	Exon 2 of 2	ENSP00000570245.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00 AC: 0 AN: 86246 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000225 AC: 3 AN: 1330890 Hom.: 0 Cov.: 31 AF XY: 0.00000307 AC XY: 2 AN XY: 650956

African (AFR) AF: 0.00 AC: 0 AN: 29182

American (AMR) AF: 0.00 AC: 0 AN: 28608

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21642

East Asian (EAS) AF: 0.00 AC: 0 AN: 33990

South Asian (SAS) AF: 0.00 AC: 0 AN: 71014

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34682

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4374

European-Non Finnish (NFE) AF: 0.00000285 AC: 3 AN: 1052192

Other (OTH) AF: 0.00 AC: 0 AN: 55206

GnomAD4 genome Cov.: 33

ExAC AF: 0.0000160 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.5
DANN	Benign	0.86
DEOGEN2	Benign	0.012	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.058	N
LIST_S2	Benign	0.43	T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.060	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.34	N
PhyloP100		-0.34
PrimateAI	Pathogenic	0.81	D
PROVEAN	Benign	-0.070	N
REVEL	Benign	0.015
Sift	Benign	0.35	T
Sift4G	Benign	0.97	T
Polyphen		0.0	B
Vest4		0.082
MutPred		0.16		Loss of glycosylation at P18 (P = 0.0035)
MVP		0.068
MPC		1.0
ClinPred		0.14	T
GERP RS		-0.80
PromoterAI		-0.036	Neutral
Varity_R		0.064
gMVP		0.14
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs768911691; hg19: chr3-142682124;