rs959

Variant names:

• chr1-70852578-T-A
• rs959
• ENST00000361210.6:n.*346A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-70852578-T-A
• chr1-70852578-T-C
• chr1-70852578-T-G

Variant summary

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

The ENST00000361210.6(PTGER3):​n.*346A>T 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 0.00000838 in 358,024 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000084 (0 hom.)
• Consequence: PTGER3 ENST00000361210.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 0 publications found

Genes affected

PTGER3 (HGNC:9595): (prostaglandin E receptor 3) The protein encoded by this gene is a member of the G-protein coupled receptor family. This protein is one of four receptors identified for prostaglandin E2 (PGE2). This receptor may have many biological functions, which involve digestion, nervous system, kidney reabsorption, and uterine contraction activities. Studies of the mouse counterpart suggest that this receptor may also mediate adrenocorticotropic hormone response as well as fever generation in response to exogenous and endogenous stimuli. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

ENSG00000235782 (HGNC:40481):

LOC102724572 (HGNC:):

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 (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NR_028292.2	n.1794A>T		non_coding_transcript_exon_variant	Exon 6 of 6
PTGER3	NR_028293.2	n.1767A>T		non_coding_transcript_exon_variant	Exon 5 of 5
PTGER3	NR_028294.2	n.1863A>T		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000361210.6	n.*346A>T		non_coding_transcript_exon_variant	Exon 6 of 6	1		ENSP00000424340.1
PTGER3	ENST00000479353.5	n.*346A>T		non_coding_transcript_exon_variant	Exon 5 of 5	1		ENSP00000421583.1
PTGER3	ENST00000497146.5	n.*346A>T		non_coding_transcript_exon_variant	Exon 6 of 6	1		ENSP00000423561.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000838 AC: 3 AN: 358024 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 188418

African (AFR) AF: 0.00 AC: 0 AN: 8644

American (AMR) AF: 0.00 AC: 0 AN: 10538

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11468

East Asian (EAS) AF: 0.00 AC: 0 AN: 24028

South Asian (SAS) AF: 0.0000329 AC: 1 AN: 30366

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26668

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1674

European-Non Finnish (NFE) AF: 0.00000895 AC: 2 AN: 223374

Other (OTH) AF: 0.00 AC: 0 AN: 21264

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs959; hg19: chr1-71318261;