rs10495903

chr2-43579779-C-T

Variant summary

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

The NM_022065.5(THADA):c.722-1172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,048 control chromosomes in the GnomAD database, including 1,297 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 0.13 (1297 hom., cov: 32)
• Consequence: THADA NM_022065.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

THADA (HGNC:19217): (THADA armadillo repeat containing) This gene is the target of 2p21 choromosomal aberrations in benign thyroid adenomas. Single nucleotide polymorphisms (SNPs) in this gene may be associated with type 2 diabetes and polycystic ovary syndrome. The encoded protein is likely involved in the death receptor pathway and apoptosis. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
THADA	NM_022065.5	c.722-1172G>A		intron_variant		ENST00000405975.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THADA	ENST00000405975.7	c.722-1172G>A		intron_variant		1	NM_022065.5	P1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19089 AN: 151930 Hom.: 1296 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00579

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.126 AC: 19113 AN: 152048 Hom.: 1297 Cov.: 32 AF XY: 0.121 AC XY: 8965 AN XY: 74330

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0795

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.00580

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0726

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.103

Alfa AF: 0.128 Hom.: 1756

Bravo AF: 0.123

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.043
Dann	Benign	0.63

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: rs10495903; hg19: chr2-43806918;