rs4318720

Positions:

• chr4-117411099-G-A

Variant summary

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

The ENST00000656637.1(LINC02263):​n.958G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,834 control chromosomes in the GnomAD database, including 1,547 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 0.13 (1547 hom., cov: 32)
• Consequence: LINC02263 ENST00000656637.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

LINC02263 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117411099G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02263	ENST00000656637.1	n.958G>A		non_coding_transcript_exon_variant	4/4
LINC01378	ENST00000667115.1	n.621G>A		non_coding_transcript_exon_variant	2/2
LINC01378	ENST00000626258.2	n.200+4734G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19293 AN: 151714 Hom.: 1538 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.127 AC: 19319 AN: 151834 Hom.: 1547 Cov.: 32 AF XY: 0.132 AC XY: 9789 AN XY: 74190

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.155

Alfa AF: 0.112 Hom.: 1526

Bravo AF: 0.132

Asia WGS AF: 0.257 AC: 892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4318720; hg19: chr4-118332255;