rs1018466

Variant names:

• chr14-36654045-A-C
• rs1018466
• ENST00000729137.1:n.1621T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-36654045-A-C
• chr14-36654045-A-G

Variant summary

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

The ENST00000729137.1(ENSG00000258661):​n.1621T>G 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 0.492 in 151,992 control chromosomes in the GnomAD database, including 18,723 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 0.49 (18723 hom., cov: 32)
• Consequence: ENSG00000258661 ENST00000729137.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

Genes affected

ENSG00000258661 (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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729137.1. 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
	ENSG00000258661	ENST00000729137.1		n.1621T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000258661	ENST00000555107.1	TSL:3	n.258+4499T>G		intron	N/A
	ENSG00000283098	ENST00000634305.1	TSL:5	n.323-704A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74787 AN: 151874 Hom.: 18713 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.492 AC: 74838 AN: 151992 Hom.: 18723 Cov.: 32 AF XY: 0.490 AC XY: 36371 AN XY: 74300

African (AFR) AF: 0.465 AC: 19291 AN: 41444

American (AMR) AF: 0.392 AC: 5984 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3468

East Asian (EAS) AF: 0.609 AC: 3146 AN: 5164

South Asian (SAS) AF: 0.427 AC: 2054 AN: 4814

European-Finnish (FIN) AF: 0.454 AC: 4794 AN: 10556

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36219 AN: 67966

Other (OTH) AF: 0.501 AC: 1057 AN: 2108

Alfa AF: 0.519 Hom.: 87513

Bravo AF: 0.489

Asia WGS AF: 0.520 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.035
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1018466; hg19: chr14-37123250;