rs17537900

Variant names:

• chr13-43121313-T-C
• rs17537900
• NR_047013.1:n.119+8030T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-43121313-T-C
• chr13-43121313-T-G

Variant summary

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

The NR_047013.1(LINC00400):​n.119+8030T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,244 control chromosomes in the GnomAD database, including 636 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 0.082 (636 hom., cov: 32)
• Consequence: LINC00400 NR_047013.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• Publications: 1 publications found

Genes affected

LINC00400 (HGNC:42729): (long intergenic non-protein coding RNA 400)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_047013.1. 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
	LINC00400	NR_047013.1		n.119+8030T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12462 AN: 152126 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0819 AC: 12468 AN: 152244 Hom.: 636 Cov.: 32 AF XY: 0.0800 AC XY: 5957 AN XY: 74436

African (AFR) AF: 0.0385 AC: 1599 AN: 41538

American (AMR) AF: 0.0674 AC: 1031 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3472

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5176

South Asian (SAS) AF: 0.110 AC: 531 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7759 AN: 68008

Other (OTH) AF: 0.0695 AC: 147 AN: 2116

Alfa AF: 0.0932 Hom.: 1171

Bravo AF: 0.0752

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.46
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs17537900; hg19: chr13-43695449;