chr4-131665703-C-A

Variant names:

• chr4-131665703-C-A
• rs1964033
• NR_183917.1:n.772-27631C>A

Variant summary

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

The NR_183917.1(LINC02377):​n.772-27631C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,942 control chromosomes in the GnomAD database, including 18,673 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 0.49 (18673 hom., cov: 32)
• Consequence: LINC02377 NR_183917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183917.1. 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.772-27631C>A		intron	N/A
	LINC02377	NR_183918.1		n.979-27631C>A		intron	N/A
	LINC02377	NR_183919.1		n.890-27631C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74654 AN: 151824 Hom.: 18668 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.492 AC: 74687 AN: 151942 Hom.: 18673 Cov.: 32 AF XY: 0.496 AC XY: 36784 AN XY: 74232

African (AFR) AF: 0.408 AC: 16904 AN: 41402

American (AMR) AF: 0.570 AC: 8712 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1657 AN: 3472

East Asian (EAS) AF: 0.573 AC: 2953 AN: 5158

South Asian (SAS) AF: 0.552 AC: 2655 AN: 4808

European-Finnish (FIN) AF: 0.528 AC: 5565 AN: 10542

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34572 AN: 67968

Other (OTH) AF: 0.479 AC: 1010 AN: 2110

Alfa AF: 0.301 Hom.: 2519

Bravo AF: 0.489

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1964033; hg19: chr4-132586858;