rs6854930

Variant names:

• chr4-174119151-C-A
• rs6854930
• ENST00000503140.2:n.343+746G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-174119151-C-A
• chr4-174119151-C-T

Variant summary

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

The ENST00000503140.2(LINC02268):​n.343+746G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,066 control chromosomes in the GnomAD database, including 1,151 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 0.11 (1151 hom., cov: 32)
• Consequence: LINC02268 ENST00000503140.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

Genes affected

LINC02268 (HGNC:53183): (long intergenic non-protein coding RNA 2268)

ENSG00000295367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02268	NR_125896.1	n.275+746G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02268	ENST00000503140.2	n.343+746G>T		intron_variant	Intron 2 of 6	4
LINC02268	ENST00000515444.5	n.275+746G>T		intron_variant	Intron 2 of 4	2
LINC02268	ENST00000656529.1	n.78+746G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16866 AN: 151948 Hom.: 1150 Cov.: 32

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0980

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.111 AC: 16876 AN: 152066 Hom.: 1151 Cov.: 32 AF XY: 0.113 AC XY: 8394 AN XY: 74318

African (AFR) AF: 0.0453 AC: 1880 AN: 41494

American (AMR) AF: 0.114 AC: 1737 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3470

East Asian (EAS) AF: 0.0979 AC: 506 AN: 5170

South Asian (SAS) AF: 0.110 AC: 530 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2009 AN: 10544

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9495 AN: 67990

Other (OTH) AF: 0.103 AC: 217 AN: 2110

Alfa AF: 0.0864 Hom.: 157

Bravo AF: 0.0996

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.026
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6854930; hg19: chr4-175040302;