rs12894724

Positions:

• chr14-36522024-C-T

Variant summary

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

The NR_103710.1(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 NR_103710.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKX2-1-AS1	NR_103710.1	n.783C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKX2-1-AS1	ENST00000521292.2	n.783C>T		non_coding_transcript_exon_variant	2/2	2
	ENST00000634305.1	n.322+73187C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0357

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0703

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.0412

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12894724; hg19: chr14-36991229;