rs12589672

Variant names:

• chr14-36524701-A-T
• rs12589672
• ENST00000716762.1:n.298A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000716762.1(NKX2-1-AS1):​n.298A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 152,112 control chromosomes in the GnomAD database, including 206 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 0.042 (206 hom., cov: 33)
• Consequence: NKX2-1-AS1 ENST00000716762.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

NKX2-1-AS1 (HGNC:40585): (NKX2-1 antisense RNA 1)

LOC105370453 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716762.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKX2-1-AS1	ENST00000716762.1		n.298A>T		non_coding_transcript_exon	Exon 1 of 4
	NKX2-1-AS1	ENST00000716763.1		n.13A>T		non_coding_transcript_exon	Exon 1 of 4
	NKX2-1-AS1	ENST00000716764.1		n.11A>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6425 AN: 151994 Hom.: 207 Cov.: 33

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0423 AC: 6428 AN: 152112 Hom.: 206 Cov.: 33 AF XY: 0.0441 AC XY: 3280 AN XY: 74360

African (AFR) AF: 0.0124 AC: 514 AN: 41508

American (AMR) AF: 0.0730 AC: 1116 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3468

East Asian (EAS) AF: 0.123 AC: 634 AN: 5148

South Asian (SAS) AF: 0.0712 AC: 343 AN: 4816

European-Finnish (FIN) AF: 0.0586 AC: 621 AN: 10590

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0439 AC: 2981 AN: 67972

Other (OTH) AF: 0.0412 AC: 87 AN: 2112

Alfa AF: 0.0401 Hom.: 19

Bravo AF: 0.0438

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12589672; hg19: chr14-36993906;