rs1983667

Variant names:

• chr14-36628983-A-T
• rs1983667
• ENST00000634305.1:n.323-25766A>T

Variant summary

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

The ENST00000716761.1(NKX2-1-AS1):​n.271-25766A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,084 control chromosomes in the GnomAD database, including 1,099 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 0.087 (1099 hom., cov: 32)
• Consequence: NKX2-1-AS1 ENST00000716761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 2 publications found

Genes affected

ENSG00000283098 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716761.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283098	ENST00000634305.1	TSL:5	n.323-25766A>T		intron	N/A
	NKX2-1-AS1	ENST00000716761.1		n.271-25766A>T		intron	N/A
	NKX2-1-AS1	ENST00000716763.1		n.772-25766A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13226 AN: 151968 Hom.: 1096 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0218

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0871 AC: 13241 AN: 152084 Hom.: 1099 Cov.: 32 AF XY: 0.0846 AC XY: 6294 AN XY: 74374

African (AFR) AF: 0.227 AC: 9394 AN: 41414

American (AMR) AF: 0.0434 AC: 663 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0212 AC: 102 AN: 4814

European-Finnish (FIN) AF: 0.0345 AC: 366 AN: 10618

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2427 AN: 68002

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.0611 Hom.: 90

Bravo AF: 0.0949

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.36
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1983667; hg19: chr14-37098188;