4-131490215-T-G

Variant names:

• chr4-131490215-T-G
• rs171251
• ENST00000500169.7:n.592-37015T>G

Variant summary

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

The ENST00000500169.7(LINC02377):​n.592-37015T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,012 control chromosomes in the GnomAD database, including 7,656 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 0.30 (7656 hom., cov: 32)
• Consequence: LINC02377 ENST00000500169.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02377	NR_183917.1	n.586-37015T>G		intron_variant	Intron 1 of 4
LINC02377	NR_183918.1	n.704-32705T>G		intron_variant	Intron 2 of 7
LINC02377	NR_183919.1	n.704-37015T>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02377	ENST00000500169.7	n.592-37015T>G		intron_variant	Intron 1 of 2	3
LINC02377	ENST00000505436.1	n.118+4141T>G		intron_variant	Intron 1 of 3	5
LINC02377	ENST00000652848.1	n.706+20592T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46024 AN: 151894 Hom.: 7645 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.303 AC: 46067 AN: 152012 Hom.: 7656 Cov.: 32 AF XY: 0.296 AC XY: 22014 AN XY: 74304

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.0469

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.304

Alfa AF: 0.283 Hom.: 1283

Bravo AF: 0.313

Asia WGS AF: 0.202 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs171251; hg19: chr4-132411370;