NM_000369.5:c.392+245A>G

Variant names:

• chr14-81088273-A-G
• rs2075173
• NM_000369.5:c.392+245A>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000369.5(TSHR):​c.392+245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 152,294 control chromosomes in the GnomAD database, including 830 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.092 (830 hom., cov: 32)
• Consequence: TSHR NM_000369.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0570
• Publications: 4 publications found

Genes affected

TSHR (HGNC:12373): (thyroid stimulating hormone receptor) The protein encoded by this gene is a membrane protein and a major controller of thyroid cell metabolism. The encoded protein is a receptor for thyrothropin and thyrostimulin, and its activity is mediated by adenylate cyclase. Defects in this gene are a cause of several types of hyperthyroidism. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

TSHR Gene-Disease associations (from GenCC):

• familial gestational hyperthyroidism

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
• hypothyroidism due to TSH receptor mutations

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
• familial hyperthyroidism due to mutations in TSH receptor

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• athyreosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• thyroid hypoplasia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TSHR-AS1 (HGNC:58172):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 14-81088273-A-G is Benign according to our data. Variant chr14-81088273-A-G is described in ClinVar as Benign. ClinVar VariationId is 1283819.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000369.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSHR	NM_000369.5	MANE Select	c.392+245A>G		intron	N/A	NP_000360.2
	TSHR	NM_001142626.3		c.392+245A>G		intron	N/A	NP_001136098.1
	TSHR	NM_001018036.3		c.392+245A>G		intron	N/A	NP_001018046.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSHR	ENST00000298171.7	TSL:1 MANE Select	c.392+245A>G		intron	N/A	ENSP00000298171.2
	TSHR	ENST00000554435.1	TSL:1	c.392+245A>G		intron	N/A	ENSP00000450549.1
	TSHR	ENST00000342443.10	TSL:1	c.392+245A>G		intron	N/A	ENSP00000340113.6

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 14051 AN: 152176 Hom.: 830 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0894

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0922 AC: 14049 AN: 152294 Hom.: 830 Cov.: 32 AF XY: 0.0928 AC XY: 6912 AN XY: 74472

African (AFR) AF: 0.0275 AC: 1144 AN: 41564

American (AMR) AF: 0.0943 AC: 1443 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3472

East Asian (EAS) AF: 0.185 AC: 960 AN: 5178

South Asian (SAS) AF: 0.0890 AC: 430 AN: 4830

European-Finnish (FIN) AF: 0.0892 AC: 946 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8375 AN: 68024

Other (OTH) AF: 0.0809 AC: 171 AN: 2114

Alfa AF: 0.104 Hom.: 133

Bravo AF: 0.0915

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.82
PhyloP100		-0.057
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2075173; hg19: chr14-81554617;