14-36517091-A-AGGGTTG

Variant names:

• chr14-36517091-A-AGGGTTG
• rs141117763
• NM_001079668.3:c.*186_*187insCAACCC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001079668.3(NKX2-1):​c.*186_*187insCAACCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 876,714 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 28)
  • Exomes 𝑓: 0.000013 (0 hom.)
• Consequence: NKX2-1 NM_001079668.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 publications found

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]

SFTA3 (HGNC:):

SFTA3 (HGNC:18387): (surfactant associated 3) Involved in wound healing. Located in cytoplasm and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKX2-1	NM_001079668.3	c.*186_*187insCAACCC		3_prime_UTR_variant	Exon 3 of 3	ENST00000354822.7	NP_001073136.1
NKX2-1	NM_003317.4	c.*186_*187insCAACCC		3_prime_UTR_variant	Exon 2 of 2		NP_003308.1
SFTA3	NR_161364.1	n.89+2376_89+2377insCAACCC		intron_variant	Intron 1 of 4
SFTA3	NR_161365.1	n.89+2376_89+2377insCAACCC		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKX2-1	ENST00000354822.7	c.*186_*187insCAACCC		3_prime_UTR_variant	Exon 3 of 3	1	NM_001079668.3	ENSP00000346879.6
SFTA3	ENST00000546983.2	n.373+1893_373+1894insCAACCC		intron_variant	Intron 2 of 3	4		ENSP00000449302.2

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 0.0000125 AC: 11 AN: 876714 Hom.: 0 Cov.: 12 AF XY: 0.0000186 AC XY: 8 AN XY: 430774

African (AFR) AF: 0.00 AC: 0 AN: 19890

American (AMR) AF: 0.0000798 AC: 1 AN: 12532

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14660

East Asian (EAS) AF: 0.00 AC: 0 AN: 27734

South Asian (SAS) AF: 0.00 AC: 0 AN: 41152

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27754

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2668

European-Non Finnish (NFE) AF: 0.0000130 AC: 9 AN: 691942

Other (OTH) AF: 0.0000261 AC: 1 AN: 38382

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.089

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs141117763; hg19: chr14-36986296;