rs168427

Positions:

• chr4-131597617-A-G
• chr4-131597617-A-T

Variant summary

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

The NR_183917.1(LINC02377):​n.645-24258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,024 control chromosomes in the GnomAD database, including 4,778 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 (4778 hom., cov: 33)
• Consequence: LINC02377 NR_183917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573

Genes affected

LINC02377 (HGNC:53300): (long intergenic non-protein coding RNA 2377)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02377	NR_183917.1	n.645-24258A>G		intron_variant
LINC02377	NR_183918.1	n.852-24258A>G		intron_variant
LINC02377	NR_183919.1	n.763-24258A>G		intron_variant
LINC02377	NR_183920.1	n.785-95717A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36474 AN: 151906 Hom.: 4781 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.240 AC: 36474 AN: 152024 Hom.: 4778 Cov.: 33 AF XY: 0.243 AC XY: 18036 AN XY: 74320

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.244

Alfa AF: 0.246 Hom.: 1129

Bravo AF: 0.249

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs168427; hg19: chr4-132518772;