ENST00000795233.1:n.70G>T

Variant names:

• chr10-99532698-C-A
• rs10883371
• ENST00000795233.1:n.70G>T

Variant summary

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

The ENST00000795233.1(LINC01475):​n.70G>T 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 0.537 in 152,010 control chromosomes in the GnomAD database, including 22,103 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 0.54 (22103 hom., cov: 32)
• Consequence: LINC01475 ENST00000795233.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 17 publications found

Genes affected

LINC01475 (HGNC:51113): (long intergenic non-protein coding RNA 1475)

NKX2-3 (HGNC:7836): (NK2 homeobox 3) This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795233.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKX2-3	NM_145285.3	MANE Select	c.-434C>A		upstream_gene	N/A	NP_660328.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01475	ENST00000795233.1		n.70G>T		non_coding_transcript_exon	Exon 1 of 3
	LINC01475	ENST00000795234.1		n.84G>T		non_coding_transcript_exon	Exon 1 of 2
	NKX2-3	ENST00000344586.9	TSL:2 MANE Select	c.-434C>A		upstream_gene	N/A	ENSP00000342828.7

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81531 AN: 151892 Hom.: 22071 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.537 AC: 81611 AN: 152010 Hom.: 22103 Cov.: 32 AF XY: 0.539 AC XY: 40056 AN XY: 74304

African (AFR) AF: 0.563 AC: 23325 AN: 41438

American (AMR) AF: 0.572 AC: 8751 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1593 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2859 AN: 5164

South Asian (SAS) AF: 0.625 AC: 3011 AN: 4816

European-Finnish (FIN) AF: 0.511 AC: 5398 AN: 10554

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35043 AN: 67956

Other (OTH) AF: 0.500 AC: 1058 AN: 2114

Alfa AF: 0.463 Hom.: 2234

Bravo AF: 0.541

Asia WGS AF: 0.600 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.99
DANN	Benign	0.83
PhyloP100		-1.2
PromoterAI		0.021	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10883371; hg19: chr10-101292455;