13-74553977-C-T

Position:

• chr13-74553977-C-T

Variant summary

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

The NR_034024.1(LINC00347):​n.62-636C>T 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 0.0861 in 152,204 control chromosomes in the GnomAD database, including 602 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 0.086 (602 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC00347 NR_034024.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

LINC00347 (HGNC:27890): (long intergenic non-protein coding RNA 347)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00347	NR_034024.1	n.62-636C>T		intron_variant, non_coding_transcript_variant
LINC00347	NR_034025.1	n.62-680C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00347	ENST00000594461.2	n.349-636C>T		intron_variant, non_coding_transcript_variant		1
LINC00347	ENST00000601480.1	n.13C>T		non_coding_transcript_exon_variant	1/2	2
LINC00347	ENST00000451336.2	n.62-680C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0859 AC: 13059 AN: 152082 Hom.: 593 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0898

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0861 AC: 13101 AN: 152200 Hom.: 602 Cov.: 32 AF XY: 0.0854 AC XY: 6357 AN XY: 74416

Gnomad4 AFR AF: 0.0871

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0294

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.0944

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0903 Hom.: 624

Bravo AF: 0.0835

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.070
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17718828; hg19: chr13-75128114;