rs7829028

chr8-109097301-C-T

Variant summary

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

The NM_003301.7(TRHR):c.789+9000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,018 control chromosomes in the GnomAD database, including 5,753 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 0.21 (5753 hom., cov: 32)
• Consequence: TRHR NM_003301.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

Genes affected

TRHR (HGNC:12299): (thyrotropin releasing hormone receptor) This gene encodes a G protein-coupled receptor for thyrotropin-releasing hormone (TRH). Upon binding to TRH, this receptor activates the inositol phospholipid-calcium-protein kinase C transduction pathway. Mutations in this gene have been associated with generalized thyrotropin-releasing hormone resistance. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRHR	NM_003301.7	c.789+9000C>T		intron_variant		ENST00000518632.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRHR	ENST00000518632.2	c.789+9000C>T		intron_variant		5	NM_003301.7	P1
TRHR	ENST00000311762.2	c.789+9000C>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32108 AN: 151900 Hom.: 5718 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0453

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.212 AC: 32195 AN: 152018 Hom.: 5753 Cov.: 32 AF XY: 0.210 AC XY: 15581 AN XY: 74304

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0449

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0828

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.205

Alfa AF: 0.156 Hom.: 542

Bravo AF: 0.228

Asia WGS AF: 0.144 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.5
Dann	Benign	0.31

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: rs7829028; hg19: chr8-110109530;