rs1505287

chr3-24371199-G-Achr3-24371199-G-T

Variant summary

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

The NM_001354712.2(THRB):c.-260-33828C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,742 control chromosomes in the GnomAD database, including 8,496 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 0.30 (8496 hom., cov: 31)
• Consequence: THRB NM_001354712.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

THRB (HGNC:11799): (thyroid hormone receptor beta) The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Mutations in this gene are known to be a cause of generalized thyroid hormone resistance (GTHR), a syndrome characterized by goiter and high levels of circulating thyroid hormone (T3-T4), with normal or slightly elevated thyroid stimulating hormone (TSH). Several alternatively spliced transcript variants encoding the same protein have been observed for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THRB	NM_001354712.2	c.-260-33828C>T		intron_variant		ENST00000646209.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THRB	ENST00000646209.2	c.-260-33828C>T		intron_variant			NM_001354712.2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45876 AN: 151622 Hom.: 8490 Cov.: 31

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.302 AC: 45896 AN: 151742 Hom.: 8496 Cov.: 31 AF XY: 0.312 AC XY: 23136 AN XY: 74122

Gnomad4 AFR AF: 0.0940

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.274

Alfa AF: 0.335 Hom.: 2076

Bravo AF: 0.281

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	9.6
Dann	Benign	0.46

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: rs1505287; hg19: chr3-24412690;