rs17110690

Variant names:

• chr12-72014217-G-A
• rs17110690
• NM_173353.4:c.1069-8182G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-72014217-G-A
• chr12-72014217-G-T

Variant summary

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

The NM_173353.4(TPH2):​c.1069-8182G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,768 control chromosomes in the GnomAD database, including 3,148 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 0.19 (3148 hom., cov: 30)
• Consequence: TPH2 NM_173353.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

TPH2 (HGNC:20692): (tryptophan hydroxylase 2) This gene encodes a member of the pterin-dependent aromatic acid hydroxylase family. The encoded protein catalyzes the first and rate limiting step in the biosynthesis of serotonin, an important hormone and neurotransmitter. Mutations in this gene may be associated with psychiatric diseases such as bipolar affective disorder and major depression. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPH2	NM_173353.4	c.1069-8182G>A		intron_variant	Intron 8 of 10	ENST00000333850.4	NP_775489.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TPH2	ENST00000333850.4	c.1069-8182G>A		intron_variant	Intron 8 of 10	1	NM_173353.4	ENSP00000329093.3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29587 AN: 151650 Hom.: 3152 Cov.: 30

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.195 AC: 29583 AN: 151768 Hom.: 3148 Cov.: 30 AF XY: 0.197 AC XY: 14599 AN XY: 74170

Gnomad4 AFR AF: 0.0991

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.199

Alfa AF: 0.210 Hom.: 4932

Bravo AF: 0.190

Asia WGS AF: 0.204 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.36

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

Publications

LitVar

Other links and lift over

dbSNP: rs17110690; hg19: chr12-72407997;