13-91089667-C-T

Position:

• chr13-91089667-C-T

Variant summary

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

The NR_104057.1(LINC00380):​n.22-50G>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 0.607 in 151,976 control chromosomes in the GnomAD database, including 29,305 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 (29305 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00380 NR_104057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

LINC00380 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00380	NR_104057.1	n.22-50G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92114 AN: 151858 Hom.: 29244 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.607 AC: 92234 AN: 151976 Hom.: 29305 Cov.: 32 AF XY: 0.617 AC XY: 45864 AN XY: 74280

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.552

Alfa AF: 0.518 Hom.: 32839

Bravo AF: 0.609

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs898271; hg19: chr13-91741921;