rs34836514

Variant names:

• chr12-11054586-G-A
• rs34836514
• ENST00000536668.2:n.-164-7398C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-11054586-G-A
• chr12-11054586-G-C
• chr12-11054586-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536668.2(ENSG00000275778):​n.-164-7398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 149,336 control chromosomes in the GnomAD database, including 3,998 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 0.22 (3998 hom., cov: 32)
• Consequence: ENSG00000275778 ENST00000536668.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 3 publications found

Genes affected

ENSG00000275778 (HGNC:):

PRH1 (HGNC:9366): (proline rich protein HaeIII subfamily 1) This gene encodes a member of the heterogeneous family of proline-rich salivary glycoproteins. The encoded preproprotein undergoes proteolytic processing to generate one or more mature isoforms before secretion from the parotid and submandibular/sublingual glands. Multiple distinct alleles of this locus including the parotid isoelectric-focusing variant slow (PIF-s), the parotid acidic protein (Pa), and the double band slow (Db-s) isoforms have been characterized. The reference genome encodes the Db-s allele. Certain alleles of this gene are associated with susceptibility to dental caries. This gene is located in a cluster of closely related salivary proline-rich proteins on chromosome 12. Co-transcription of this gene with adjacent genes has been observed. Alternate splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]

PRR4 (HGNC:18020): (proline rich 4) This gene encodes a member of the proline-rich protein family that lacks a conserved repetitive domain. This protein may play a role in protective functions in the eye. Alternative splicing result in multiple transcript variants. Read-through transcription also exists between this gene and the upstream PRH1 (proline-rich protein HaeIII subfamily 1) gene. [provided by RefSeq, Feb 2011]

TAS2R14 (HGNC:14920): (taste 2 receptor member 14) This gene product belongs to the family of candidate taste receptors that are members of the G-protein-coupled receptor superfamily. These proteins are specifically expressed in the taste receptor cells of the tongue and palate epithelia. They are organized in the genome in clusters and are genetically linked to loci that influence bitter perception in mice and humans. In functional expression studies, they respond to bitter tastants. This gene maps to the taste receptor gene cluster on chromosome 12p13. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRH1	NM_001291315.2	c.-133-7398C>T		intron_variant	Intron 1 of 5		NP_001278244.1
PRH1	NM_001291314.2	c.-294-7398C>T		intron_variant	Intron 1 of 6		NP_001278243.1
PRH1-TAS2R14	NM_001316893.2	c.-133-7398C>T		intron_variant	Intron 1 of 4		NP_001303822.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275778	ENST00000536668.2	n.-164-7398C>T		intron_variant	Intron 1 of 9	5		ENSP00000482961.1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32174 AN: 149220 Hom.: 4001 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.197

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.215 AC: 32174 AN: 149336 Hom.: 3998 Cov.: 32 AF XY: 0.213 AC XY: 15522 AN XY: 72802

African (AFR) AF: 0.133 AC: 5437 AN: 40934

American (AMR) AF: 0.217 AC: 3241 AN: 14926

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 508 AN: 3406

East Asian (EAS) AF: 0.00406 AC: 20 AN: 4928

South Asian (SAS) AF: 0.0564 AC: 259 AN: 4594

European-Finnish (FIN) AF: 0.329 AC: 3343 AN: 10162

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.275 AC: 18472 AN: 67108

Other (OTH) AF: 0.195 AC: 406 AN: 2078

Alfa AF: 0.211 Hom.: 1397

Bravo AF: 0.202

Asia WGS AF: 0.0490 AC: 172 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		0.024

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: rs34836514; hg19: chr12-11207185;