rs4864039

Variant names:

• chr4-131384419-G-A
• rs4864039
• ENST00000500169.7:n.591+4078G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-131384419-G-A
• chr4-131384419-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500169.7(LINC02377):​n.591+4078G>A variant causes a intron 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 ENST00000500169.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02377	NR_183917.1	n.585+4078G>A		intron_variant	Intron 1 of 4
LINC02377	NR_183918.1	n.585+4078G>A		intron_variant	Intron 1 of 7
LINC02377	NR_183919.1	n.585+4078G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02377	ENST00000500169.7	n.591+4078G>A		intron_variant	Intron 1 of 2	3
LINC02377	ENST00000652848.1	n.625+4078G>A		intron_variant	Intron 1 of 2
LINC02377	ENST00000654488.1	n.582+4078G>A		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.703 AC: 29038 AN: 41330

American (AMR) AF: 0.539 AC: 8200 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1957 AN: 3464

East Asian (EAS) AF: 0.557 AC: 2857 AN: 5132

South Asian (SAS) AF: 0.625 AC: 3005 AN: 4810

European-Finnish (FIN) AF: 0.541 AC: 5659 AN: 10466

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38728 AN: 67890

Other (OTH) AF: 0.617 AC: 1296 AN: 2102

Alfa AF: 0.584 Hom.: 68550

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4864039; hg19: chr4-132305574;