rs34122827

chr13-63204644-AACTT-Achr13-63204644-AACTT-AACTTACTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_126409.1(LINC00376):n.424-10117_424-10114del 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 0.39 in 151,740 control chromosomes in the GnomAD database, including 12,344 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (12344 hom., cov: 0)
• Consequence: LINC00376 NR_126409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

Genes affected

LINC00376 (HGNC:42701): (long intergenic non-protein coding RNA 376)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00376	NR_126409.1	n.424-10117_424-10114del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00376	ENST00000439454.3	n.459-10117_459-10114del		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59244 AN: 151622 Hom.: 12347 Cov.: 0

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.390 AC: 59246 AN: 151740 Hom.: 12344 Cov.: 0 AF XY: 0.381 AC XY: 28274 AN XY: 74138

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.0264

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.386

Alfa AF: 0.436 Hom.: 1827

Bravo AF: 0.385

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34122827; hg19: chr13-63778777;