rs17104630

Variant names:

• chr14-36530844-A-G
• rs17104630
• ENST00000634305.1:n.322+82007A>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.88+11165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,282 control chromosomes in the GnomAD database, including 633 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 0.081 (633 hom., cov: 33)
• Consequence: NKX2-1-AS1 ENST00000716761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 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.322+82007A>G		intron	N/A
	NKX2-1-AS1	ENST00000716761.1		n.88+11165A>G		intron	N/A
	NKX2-1-AS1	ENST00000716762.1		n.805+5636A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12312 AN: 152164 Hom.: 629 Cov.: 33

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0809 AC: 12323 AN: 152282 Hom.: 633 Cov.: 33 AF XY: 0.0838 AC XY: 6243 AN XY: 74472

African (AFR) AF: 0.0313 AC: 1300 AN: 41562

American (AMR) AF: 0.137 AC: 2098 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.187 AC: 970 AN: 5174

South Asian (SAS) AF: 0.113 AC: 545 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1138 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0859 AC: 5846 AN: 68026

Other (OTH) AF: 0.0809 AC: 171 AN: 2114

Alfa AF: 0.0835 Hom.: 1258

Bravo AF: 0.0813

Asia WGS AF: 0.130 AC: 449 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	0.36
DANN	Benign	0.35
PhyloP100		-0.92

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: rs17104630;

hg19: chr14-37000049;