4-131465802-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500169.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02377	NR_183917.1		n.586-61428T>C		intron	N/A
	LINC02377	NR_183918.1		n.703+38185T>C		intron	N/A
	LINC02377	NR_183919.1		n.703+38185T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02377	ENST00000500169.7	TSL:3	n.592-61428T>C		intron	N/A
	LINC02377	ENST00000652848.1		n.626-3741T>C		intron	N/A
	LINC02377	ENST00000654488.1		n.700+38185T>C		intron	N/A

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

African (AFR) AF: 0.333 AC: 13739 AN: 41286

American (AMR) AF: 0.230 AC: 3481 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3468

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5178

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4806

European-Finnish (FIN) AF: 0.181 AC: 1871 AN: 10340

Middle Eastern (MID) AF: 0.314 AC: 91 AN: 290

European-Non Finnish (NFE) AF: 0.243 AC: 16489 AN: 67776

Other (OTH) AF: 0.276 AC: 578 AN: 2092

Alfa AF: 0.222 Hom.: 2079

Bravo AF: 0.263

Asia WGS AF: 0.169 AC: 588 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.53
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1299288;

hg19: chr4-132386957;