rs1299288

Variant names:

• chr4-131465802-T-A
• rs1299288
• ENST00000500169.7:n.592-61428T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-131465802-T-A
• chr4-131465802-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000500169.7(LINC02377):​n.592-61428T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000528 in 151,420 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000053 (0 hom., cov: 31)
• Consequence: LINC02377 ENST00000500169.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02377	NR_183917.1	n.586-61428T>A		intron_variant	Intron 1 of 4
LINC02377	NR_183918.1	n.703+38185T>A		intron_variant	Intron 2 of 7
LINC02377	NR_183919.1	n.703+38185T>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02377	ENST00000500169.7	n.592-61428T>A		intron_variant	Intron 1 of 2	3
LINC02377	ENST00000652848.1	n.626-3741T>A		intron_variant	Intron 1 of 2
LINC02377	ENST00000654488.1	n.700+38185T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0000463 AC: 7 AN: 151308 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000170

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000528 AC: 8 AN: 151420 Hom.: 0 Cov.: 31 AF XY: 0.0000405 AC XY: 3 AN XY: 74034

African (AFR) AF: 0.000194 AC: 8 AN: 41332

American (AMR) AF: 0.00 AC: 0 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10352

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67816

Other (OTH) AF: 0.00 AC: 0 AN: 2096

Alfa AF: 0.00 Hom.: 2079

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.49
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1299288; hg19: chr4-132386957;