rs1413463

chr13-89251637-T-A

Variant summary

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

The NR_047025.1(LINC00440):n.68+16279T>A 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 0.612 in 151,908 control chromosomes in the GnomAD database, including 30,715 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 0.61 (30715 hom., cov: 32)
• Consequence: LINC00440 NR_047025.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

Genes affected

LINC00440 (HGNC:42777): (long intergenic non-protein coding RNA 440)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00440	NR_047025.1	n.68+16279T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00440	ENST00000653072.1	n.29-17995T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92910 AN: 151790 Hom.: 30724 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.612 AC: 92923 AN: 151908 Hom.: 30715 Cov.: 32 AF XY: 0.602 AC XY: 44710 AN XY: 74238

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.664

Alfa AF: 0.669 Hom.: 4418

Bravo AF: 0.601

Asia WGS AF: 0.485 AC: 1687 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1413463; hg19: chr13-89903891;