rs7955501

chr12-71956246-T-Achr12-71956246-T-G

Variant summary

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

The NM_173353.4(TPH2):c.608+6591T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,026 control chromosomes in the GnomAD database, including 26,144 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 0.58 (26144 hom., cov: 31)
• Consequence: TPH2 NM_173353.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPH2	NM_173353.4	c.608+6591T>A		intron_variant		ENST00000333850.4
TPH2	XR_001748575.2	n.751-5307T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPH2	ENST00000333850.4	c.608+6591T>A		intron_variant		1	NM_173353.4	P1
TPH2	ENST00000546576.1	n.619-5307T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88601 AN: 151908 Hom.: 26112 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.583 AC: 88682 AN: 152026 Hom.: 26144 Cov.: 31 AF XY: 0.586 AC XY: 43527 AN XY: 74302

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.613

Alfa AF: 0.584 Hom.: 3083

Bravo AF: 0.582

Asia WGS AF: 0.676 AC: 2348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.4
Dann	Benign	0.78

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: rs7955501; hg19: chr12-72350026;