4-131465802-T-C

Position:

• chr4-131465802-T-C

Variant summary

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

The ENST00000500169.7(LINC02377):​n.592-61428T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,296 control chromosomes in the GnomAD database, including 5,231 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 0.26 (5231 hom., cov: 31)
• Consequence: LINC02377 ENST00000500169.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

Genes affected

LINC02377 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02377	NR_183917.1	n.586-61428T>C		intron_variant
LINC02377	NR_183918.1	n.703+38185T>C		intron_variant
LINC02377	NR_183919.1	n.703+38185T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02377	ENST00000500169.7	n.592-61428T>C		intron_variant		3
LINC02377	ENST00000652848.1	n.626-3741T>C		intron_variant
LINC02377	ENST00000654488.1	n.700+38185T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38587 AN: 151184 Hom.: 5226 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.255 AC: 38614 AN: 151296 Hom.: 5231 Cov.: 31 AF XY: 0.250 AC XY: 18516 AN XY: 73974

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.276

Alfa AF: 0.221 Hom.: 1882

Bravo AF: 0.263

Asia WGS AF: 0.169 AC: 588 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1299288; hg19: chr4-132386957;