rs4864039

chr4-131384419-G-Achr4-131384419-G-C

Variant summary

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

The NR_183920.1(LINC02377):n.585+4078G>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 0.604 in 151,610 control chromosomes in the GnomAD database, including 27,994 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 0.60 (27994 hom., cov: 30)
• Consequence: LINC02377 NR_183920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02377	NR_183920.1	n.585+4078G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02377	ENST00000654488.1	n.582+4078G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91398 AN: 151490 Hom.: 27943 Cov.: 30

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.604 AC: 91520 AN: 151610 Hom.: 27994 Cov.: 30 AF XY: 0.601 AC XY: 44505 AN XY: 74044

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.617

Alfa AF: 0.577 Hom.: 40178

Bravo AF: 0.608

Asia WGS AF: 0.631 AC: 2193 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.73
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4864039; hg19: chr4-132305574;