rs1872824

Positions:

• chr12-72036534-A-G

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 0.543 in 152,068 control chromosomes in the GnomAD database, including 24,264 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 0.54 (24264 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.72036534A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TPH2	ENST00000547278.1	n.78+5143A>G		intron_variant		3
TPH2	ENST00000547348.5	n.100+5143A>G		intron_variant		3
TPH2	ENST00000550403.5	n.120+5143A>G		intron_variant		3
TPH2	ENST00000551074.5	n.93+5143A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82521 AN: 151948 Hom.: 24254 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.543 AC: 82559 AN: 152068 Hom.: 24264 Cov.: 32 AF XY: 0.546 AC XY: 40619 AN XY: 74330

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.564

Alfa AF: 0.618 Hom.: 27706

Bravo AF: 0.525

Asia WGS AF: 0.523 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.62
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872824; hg19: chr12-72430314;