rs10492467

chr13-71167260-T-Cchr13-71167260-T-G

Variant summary

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

The NR_047699.1(LINC00348):n.160-110T>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 0.239 in 151,992 control chromosomes in the GnomAD database, including 8,045 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 0.24 (8045 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00348 NR_047699.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

Genes affected

LINC00348 (HGNC:42658): (long intergenic non-protein coding RNA 348)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00348	NR_047699.1	n.160-110T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00348	ENST00000655045.1	n.424-110T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36280 AN: 151874 Hom.: 8016 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.239 AC: 36367 AN: 151992 Hom.: 8045 Cov.: 32 AF XY: 0.235 AC XY: 17427 AN XY: 74302

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0618

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.205

Alfa AF: 0.118 Hom.: 2433

Bravo AF: 0.262

Asia WGS AF: 0.162 AC: 564 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.17
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492467; hg19: chr13-71741392;