rs17786733

chr2-1407157-T-A

Variant summary

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

The ENST00000497517.6(TPO):n.180+32755T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,044 control chromosomes in the GnomAD database, including 12,134 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 0.40 (12134 hom., cov: 33)
• Consequence: TPO ENST00000497517.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

Genes affected

TPO (HGNC:12015): (thyroid peroxidase) This gene encodes a membrane-bound glycoprotein. The encoded protein acts as an enzyme and plays a central role in thyroid gland function. The protein functions in the iodination of tyrosine residues in thyroglobulin and phenoxy-ester formation between pairs of iodinated tyrosines to generate the thyroid hormones, thyroxine and triiodothyronine. Mutations in this gene are associated with several disorders of thyroid hormonogenesis, including congenital hypothyroidism, congenital goiter, and thyroid hormone organification defect IIA. Multiple transcript variants encoding distinct isoforms have been identified for this gene, but the full-length nature of some variants has not been determined. [provided by RefSeq, May 2011]

(HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPO	XM_024453089.2	c.-417+101T>A		intron_variant
TPO	XM_047445652.1	c.-417+101T>A		intron_variant
TPO	XM_047445653.1	c.-417+101T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPO	ENST00000497517.6	n.180+32755T>A		intron_variant, non_coding_transcript_variant		1
	ENST00000650512.1	n.865+2372A>T		intron_variant, non_coding_transcript_variant
TPO	ENST00000650224.1	n.497+101T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60538 AN: 151926 Hom.: 12125 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.398 AC: 60576 AN: 152044 Hom.: 12134 Cov.: 33 AF XY: 0.399 AC XY: 29626 AN XY: 74322

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.393

Alfa AF: 0.401 Hom.: 1535

Bravo AF: 0.400

Asia WGS AF: 0.415 AC: 1443 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	2.1
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17786733; hg19: chr2-1410929;