rs211105

chr11-18033757-T-G

Variant summary

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

The NM_004179.3(TPH1):c.302-383A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,154 control chromosomes in the GnomAD database, including 3,380 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 (3380 hom., cov: 32)
• Consequence: TPH1 NM_004179.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483

Genes affected

TPH1 (HGNC:12008): (tryptophan hydroxylase 1) This gene encodes a member of the aromatic amino 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 have been associated with an elevated risk for a variety of diseases and disorders, including schizophrenia, somatic anxiety, anger-related traits, bipolar disorder, suicidal behavior, addictions, and others.[provided by RefSeq, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPH1	NM_004179.3	c.302-383A>C		intron_variant		ENST00000682019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPH1	ENST00000682019.1	c.302-383A>C		intron_variant			NM_004179.3	P1
TPH1	ENST00000250018.6	c.302-383A>C		intron_variant		1		P1
TPH1	ENST00000417164.5	c.302-383A>C		intron_variant, NMD_transcript_variant		1
TPH1	ENST00000528338.1	c.332-383A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29228 AN: 152036 Hom.: 3378 Cov.: 32

Gnomad AFR AF: 0.0679

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.192 AC: 29232 AN: 152154 Hom.: 3380 Cov.: 32 AF XY: 0.194 AC XY: 14427 AN XY: 74392

Gnomad4 AFR AF: 0.0678

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.211

Alfa AF: 0.230 Hom.: 1198

Bravo AF: 0.181

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.1
Dann	Benign	0.55

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: rs211105; hg19: chr11-18055304;