4-131574942-A-G

Variant names:

• chr4-131574942-A-G
• rs350993
• ENST00000654488.1:n.849-16328A>G

Variant summary

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

The ENST00000654488.1(LINC02377):​n.849-16328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,752 control chromosomes in the GnomAD database, including 28,143 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 0.59 (28143 hom., cov: 31)
• Consequence: LINC02377 ENST00000654488.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654488.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02377	NR_183917.1		n.645-46933A>G		intron	N/A
	LINC02377	NR_183918.1		n.852-46933A>G		intron	N/A
	LINC02377	NR_183919.1		n.763-46933A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02377	ENST00000654488.1		n.849-16328A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90271 AN: 151634 Hom.: 28151 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.595 AC: 90281 AN: 151752 Hom.: 28143 Cov.: 31 AF XY: 0.597 AC XY: 44260 AN XY: 74172

African (AFR) AF: 0.409 AC: 16935 AN: 41390

American (AMR) AF: 0.669 AC: 10153 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2215 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2216 AN: 5148

South Asian (SAS) AF: 0.680 AC: 3282 AN: 4824

European-Finnish (FIN) AF: 0.685 AC: 7231 AN: 10562

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46085 AN: 67868

Other (OTH) AF: 0.593 AC: 1249 AN: 2106

Alfa AF: 0.654 Hom.: 43668

Bravo AF: 0.583

Asia WGS AF: 0.547 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.46
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs350993; hg19: chr4-132496097;