14-36517069-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_001079668.3(NKX2-1):c.*209T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 834,346 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0031 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0036 (6 hom.)
• Consequence: NKX2-1 NM_001079668.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.00700

Genes affected

NKX2-1 (HGNC:11825): (NK2 homeobox 1) This gene encodes a protein initially identified as a thyroid-specific transcription factor. The encoded protein binds to the thyroglobulin promoter and regulates the expression of thyroid-specific genes but has also been shown to regulate the expression of genes involved in morphogenesis. Mutations and deletions in this gene are associated with benign hereditary chorea, choreoathetosis, congenital hypothyroidism, and neonatal respiratory distress, and may be associated with thyroid cancer. Multiple transcript variants encoding different isoforms have been found for this gene. This gene shares the symbol/alias 'TTF1' with another gene, transcription termination factor 1, which plays a role in ribosomal gene transcription. [provided by RefSeq, Feb 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 14-36517069-A-T is Benign according to our data. Variant chr14-36517069-A-T is described in ClinVar as [Benign]. Clinvar id is 313134.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00308 (461/149550) while in subpopulation AFR AF= 0.00801 (327/40816). AF 95% confidence interval is 0.0073. There are 3 homozygotes in gnomad4. There are 231 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd at 455 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKX2-1	NM_001079668.3	c.*209T>A		3_prime_UTR_variant	3/3	ENST00000354822.7
SFTA3	NR_161364.1	n.89+2399T>A		intron_variant, non_coding_transcript_variant
NKX2-1	NM_003317.4	c.*209T>A		3_prime_UTR_variant	2/2
SFTA3	NR_161365.1	n.89+2399T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKX2-1	ENST00000354822.7	c.*209T>A		3_prime_UTR_variant	3/3	1	NM_001079668.3	P4
NKX2-1	ENST00000498187.6	c.*209T>A		3_prime_UTR_variant	2/2	1		A1
	ENST00000634305.1	n.322+68232A>T		intron_variant, non_coding_transcript_variant		5
NKX2-1	ENST00000518149.5	c.*209T>A		3_prime_UTR_variant	3/3	5		A1

Frequencies

GnomAD3 genomes AF: 0.00304 AC: 455 AN: 149440 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00791

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00128

Gnomad ASJ AF: 0.000291

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.00612

Gnomad FIN AF: 0.00139

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000789

Gnomad OTH AF: 0.00148

GnomAD4 exome AF: 0.00360 AC: 2464 AN: 684796 Hom.: 6 Cov.: 11 AF XY: 0.00379 AC XY: 1282 AN XY: 338626

Gnomad4 AFR exome AF: 0.0109

Gnomad4 AMR exome AF: 0.00352

Gnomad4 ASJ exome AF: 0.00129

Gnomad4 EAS exome AF: 0.00371

Gnomad4 SAS exome AF: 0.0115

Gnomad4 FIN exome AF: 0.00295

Gnomad4 NFE exome AF: 0.00292

Gnomad4 OTH exome AF: 0.00364

GnomAD4 genome AF: 0.00308 AC: 461 AN: 149550 Hom.: 3 Cov.: 33 AF XY: 0.00317 AC XY: 231 AN XY: 72972

Gnomad4 AFR AF: 0.00801

Gnomad4 AMR AF: 0.00127

Gnomad4 ASJ AF: 0.000291

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.00612

Gnomad4 FIN AF: 0.00139

Gnomad4 NFE AF: 0.000789

Gnomad4 OTH AF: 0.00196

Alfa AF: 0.00175 Hom.: 1

Bravo AF: 0.00317

Asia WGS AF: 0.0100 AC: 35 AN: 3470

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Brain-lung-thyroid syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2022

NKX2-1: BS1, BS2 -

Benign hereditary chorea Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.37
Dann	Benign	0.55

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: rs572546897; hg19: chr14-36986274; COSMIC: COSV61387547; COSMIC: COSV61387547;