5-153891516-C-T

Position:

• chr5-153891516-C-T

Variant summary

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

The NR_146729.1(LINC01861):​n.501+4025G>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 0.552 in 152,000 control chromosomes in the GnomAD database, including 23,408 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 0.55 (23408 hom., cov: 32)
• Consequence: LINC01861 NR_146729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

LINC01861 (HGNC:52680): (long intergenic non-protein coding RNA 1861)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01861	NR_146729.1	n.501+4025G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01861	ENST00000509568.1	n.501+4025G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83739 AN: 151880 Hom.: 23368 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.552 AC: 83829 AN: 152000 Hom.: 23408 Cov.: 32 AF XY: 0.556 AC XY: 41329 AN XY: 74304

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.541

Alfa AF: 0.539 Hom.: 4185

Bravo AF: 0.558

Asia WGS AF: 0.599 AC: 2081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.078
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs919221; hg19: chr5-153271076;