rs17537900

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047013.1(LINC00400):​n.119+8030T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666

Genes affected

LINC00400 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00400	NR_047013.1	n.119+8030T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0668 Hom.: 132

Bravo AF: 0.0752

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17537900; hg19: chr13-43695449;