4-131495423-C-T

Variant names:

• chr4-131495423-C-T
• rs351089
• ENST00000500169.7:n.592-31807C>T

Variant summary

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

The ENST00000500169.7(LINC02377):​n.592-31807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 152,194 control chromosomes in the GnomAD database, including 70,517 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 0.96 (70517 hom., cov: 30)
• Consequence: LINC02377 ENST00000500169.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.983 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.586-31807C>T		intron	N/A
	LINC02377	NR_183918.1		n.704-27497C>T		intron	N/A
	LINC02377	NR_183919.1		n.704-31807C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02377	ENST00000500169.7	TSL:3	n.592-31807C>T		intron	N/A
	LINC02377	ENST00000505436.1	TSL:5	n.118+9349C>T		intron	N/A
	LINC02377	ENST00000652848.1		n.706+25800C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146207 AN: 152076 Hom.: 70471 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.961 AC: 146311 AN: 152194 Hom.: 70517 Cov.: 30 AF XY: 0.963 AC XY: 71620 AN XY: 74408

African (AFR) AF: 0.889 AC: 36909 AN: 41500

American (AMR) AF: 0.978 AC: 14947 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3411 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5164 AN: 5164

South Asian (SAS) AF: 0.984 AC: 4744 AN: 4820

European-Finnish (FIN) AF: 0.997 AC: 10584 AN: 10614

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67326 AN: 68036

Other (OTH) AF: 0.962 AC: 2025 AN: 2106

Alfa AF: 0.971 Hom.: 14700

Bravo AF: 0.956

Asia WGS AF: 0.988 AC: 3435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.63

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: rs351089;

hg19: chr4-132416578;