chr12-72058261-C-T

Position:

• chr12-72058261-C-T

Variant summary

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

The variant allele was found at a frequency of 0.511 in 151,984 control chromosomes in the GnomAD database, including 21,559 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 0.51 (21559 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.72058261C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TPH2	ENST00000547278.1	n.240+10604C>T		intron_variant		3
TPH2	ENST00000547348.5	n.202+10604C>T		intron_variant		3
TPH2	ENST00000550403.5	n.121-15332C>T		intron_variant		3
TPH2	ENST00000551074.5	n.195+10604C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77675 AN: 151866 Hom.: 21547 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.511 AC: 77717 AN: 151984 Hom.: 21559 Cov.: 32 AF XY: 0.515 AC XY: 38242 AN XY: 74284

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.527

Alfa AF: 0.579 Hom.: 5391

Bravo AF: 0.493

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1352252; hg19: chr12-72452041;