rs11897432

Positions:

• chr2-43590366-G-A

Variant summary

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

The NM_022065.5(THADA):​c.302+458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,940 control chromosomes in the GnomAD database, including 2,769 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 0.19 (2769 hom., cov: 31)
• Consequence: THADA NM_022065.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THADA	NM_022065.5	c.302+458C>T		intron_variant		ENST00000405975.7	NP_071348.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THADA	ENST00000405975.7	c.302+458C>T		intron_variant		1	NM_022065.5	ENSP00000386088	P1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28191 AN: 151822 Hom.: 2764 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.186 AC: 28200 AN: 151940 Hom.: 2769 Cov.: 31 AF XY: 0.183 AC XY: 13586 AN XY: 74260

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.0307

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.192

Alfa AF: 0.216 Hom.: 7167

Bravo AF: 0.179

Asia WGS AF: 0.114 AC: 395 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	2.2
DANN	Benign	0.79

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: rs11897432; hg19: chr2-43817505;