chr4-131565033-T-C

Position:

• chr4-131565033-T-C

Variant summary

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

The NR_183920.1(LINC02377):​n.784+95410T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,136 control chromosomes in the GnomAD database, including 2,131 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 0.16 (2131 hom., cov: 32)
• Consequence: LINC02377 NR_183920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

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 (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02377	NR_183920.1	n.784+95410T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02377	ENST00000654488.1	n.849-26237T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23968 AN: 152018 Hom.: 2131 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0755

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.157 AC: 23960 AN: 152136 Hom.: 2131 Cov.: 32 AF XY: 0.156 AC XY: 11568 AN XY: 74368

Gnomad4 AFR AF: 0.0938

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.167

Alfa AF: 0.138 Hom.: 342

Bravo AF: 0.150

Asia WGS AF: 0.0630 AC: 219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs350961; hg19: chr4-132486188;