14-36571123-T-G

Variant names:

• chr14-36571123-T-G
• rs427490
• ENST00000634305.1:n.323-83626T>G

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.270+10510T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,078 control chromosomes in the GnomAD database, including 35,058 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 0.67 (35058 hom., cov: 33)
• Consequence: NKX2-1-AS1 ENST00000716761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 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.323-83626T>G		intron	N/A
	NKX2-1-AS1	ENST00000716761.1		n.270+10510T>G		intron	N/A
	NKX2-1-AS1	ENST00000716762.1		n.1108-1054T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101792 AN: 151960 Hom.: 35036 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.670 AC: 101858 AN: 152078 Hom.: 35058 Cov.: 33 AF XY: 0.660 AC XY: 49075 AN XY: 74342

African (AFR) AF: 0.556 AC: 23050 AN: 41472

American (AMR) AF: 0.625 AC: 9551 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2147 AN: 3466

East Asian (EAS) AF: 0.547 AC: 2819 AN: 5152

South Asian (SAS) AF: 0.439 AC: 2118 AN: 4822

European-Finnish (FIN) AF: 0.701 AC: 7410 AN: 10564

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52330 AN: 68002

Other (OTH) AF: 0.690 AC: 1455 AN: 2108

Alfa AF: 0.730 Hom.: 118669

Bravo AF: 0.662

Asia WGS AF: 0.502 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.90
PhyloP100		-0.035

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs427490;

hg19: chr14-37040328;