14-36522806-C-G

Variant names:

• chr14-36522806-C-G
• rs8004831
• ENST00000521292.2:n.1565C>G

Variant summary

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

The ENST00000521292.2(NKX2-1-AS1):​n.1565C>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 0.897 in 152,428 control chromosomes in the GnomAD database, including 63,058 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 0.90 (62932 hom., cov: 32)
  • Exomes 𝑓: 0.98 (126 hom.)
• Consequence: NKX2-1-AS1 ENST00000521292.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

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

ENSG00000283098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKX2-1-AS1	NR_103710.1	n.1565C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKX2-1-AS1	ENST00000521292.2	n.1565C>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
NKX2-1-AS1	ENST00000716760.1	n.617C>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000283098	ENST00000634305.1	n.322+73969C>G		intron_variant	Intron 3 of 3	5
NKX2-1-AS1	ENST00000716761.1	n.88+3127C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136443 AN: 152052 Hom.: 62907 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.985

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.922

GnomAD4 exome AF: 0.984 AC: 254 AN: 258 Hom.: 126 Cov.: 0 AF XY: 0.989 AC XY: 176 AN XY: 178

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 8 AN: 8

South Asian (SAS) AF: 1.00 AC: 6 AN: 6

European-Finnish (FIN) AF: 1.00 AC: 22 AN: 22

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.995 AC: 195 AN: 196

Other (OTH) AF: 1.00 AC: 16 AN: 16

GnomAD4 genome AF: 0.897 AC: 136517 AN: 152170 Hom.: 62932 Cov.: 32 AF XY: 0.900 AC XY: 66964 AN XY: 74414

African (AFR) AF: 0.659 AC: 27330 AN: 41456

American (AMR) AF: 0.955 AC: 14612 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3201 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5141 AN: 5152

South Asian (SAS) AF: 0.985 AC: 4746 AN: 4818

European-Finnish (FIN) AF: 1.00 AC: 10617 AN: 10618

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67730 AN: 68032

Other (OTH) AF: 0.922 AC: 1950 AN: 2114

Alfa AF: 0.939 Hom.: 8472

Bravo AF: 0.884

Asia WGS AF: 0.967 AC: 3362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.10
DANN	Benign	0.78
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8004831; hg19: chr14-36992011;