rs12894724

Variant names:

• chr14-36522024-C-T
• rs12894724
• ENST00000521292.2:n.783C>T

Variant summary

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

The ENST00000521292.2(NKX2-1-AS1):​n.783C>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 0.0418 in 152,270 control chromosomes in the GnomAD database, including 195 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 (195 hom., cov: 32)
  • Exomes 𝑓: 0.050 (0 hom.)
• Consequence: NKX2-1-AS1 ENST00000521292.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 2 publications found

Genes affected

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

ENSG00000283098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521292.2. 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
	NKX2-1-AS1	NR_103710.1		n.783C>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKX2-1-AS1	ENST00000521292.2	TSL:2	n.783C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000283098	ENST00000634305.1	TSL:5	n.322+73187C>T		intron	N/A
	NKX2-1-AS1	ENST00000716760.1		n.89-254C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0418 AC: 6358 AN: 152112 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0393

GnomAD4 exome AF: 0.0500 AC: 2 AN: 40 Hom.: 0 Cov.: 0 AF XY: 0.0556 AC XY: 2 AN XY: 36

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0357 AC: 1 AN: 28

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.0418 AC: 6361 AN: 152230 Hom.: 195 Cov.: 32 AF XY: 0.0435 AC XY: 3240 AN XY: 74420

African (AFR) AF: 0.0127 AC: 527 AN: 41562

American (AMR) AF: 0.0731 AC: 1117 AN: 15290

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

East Asian (EAS) AF: 0.108 AC: 555 AN: 5148

South Asian (SAS) AF: 0.0703 AC: 339 AN: 4820

European-Finnish (FIN) AF: 0.0585 AC: 621 AN: 10612

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

European-Non Finnish (NFE) AF: 0.0439 AC: 2983 AN: 68014

Other (OTH) AF: 0.0412 AC: 87 AN: 2110

Alfa AF: 0.0407 Hom.: 23

Bravo AF: 0.0435

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.32
DANN	Benign	0.80
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12894724; hg19: chr14-36991229;