chr14-36522806-C-G

Position:

• chr14-36522806-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

NKX2-1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NKX2-1-AS1	NR_103710.1	n.1565C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKX2-1-AS1	ENST00000521292.2	n.1565C>G		non_coding_transcript_exon_variant	2/2	2
ENSG00000283098	ENST00000634305.1	n.322+73969C>G		intron_variant		5

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

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.995

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.922

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8004831; hg19: chr14-36992011;