14-36585106-C-T

Variant names:

• chr14-36585106-C-T
• rs177322
• ENST00000634305.1:n.323-69643C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000716761.1(NKX2-1-AS1):​n.270+24493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0622 in 152,304 control chromosomes in the GnomAD database, including 864 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 0.062 (864 hom., cov: 33)
• Consequence: NKX2-1-AS1 ENST00000716761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 6 publications found

Genes affected

ENSG00000283098 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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.323-69643C>T		intron	N/A
	NKX2-1-AS1	ENST00000716761.1		n.270+24493C>T		intron	N/A
	NKX2-1-AS1	ENST00000716763.1		n.771+12861C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9455 AN: 152186 Hom.: 861 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0267

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00304

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0622 AC: 9474 AN: 152304 Hom.: 864 Cov.: 33 AF XY: 0.0607 AC XY: 4521 AN XY: 74476

African (AFR) AF: 0.202 AC: 8408 AN: 41530

American (AMR) AF: 0.0266 AC: 407 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5186

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10632

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00304 AC: 207 AN: 68034

Other (OTH) AF: 0.0473 AC: 100 AN: 2114

Alfa AF: 0.0301 Hom.: 932

Bravo AF: 0.0707

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	22
DANN	Benign	0.77
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs177322; hg19: chr14-37054311;