rs6778854

Variant names:

• chr3-546765-A-G
• rs6778854
• ENST00000420823.5:n.97+10438A>G

Variant summary

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

The ENST00000420823.5(LINC01266):​n.97+10438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,124 control chromosomes in the GnomAD database, including 3,026 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 (3026 hom., cov: 32)
• Consequence: LINC01266 ENST00000420823.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 1 publications found

Genes affected

LINC01266 (HGNC:50309): (long intergenic non-protein coding RNA 1266)

ENSG00000287505 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000420823.5	n.97+10438A>G		intron_variant	Intron 1 of 4	2
LINC01266	ENST00000442809.1	n.75+10438A>G		intron_variant	Intron 1 of 4	4
LINC01266	ENST00000653731.1	n.49+525A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17360 AN: 152006 Hom.: 3013 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00978

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.114 AC: 17411 AN: 152124 Hom.: 3026 Cov.: 32 AF XY: 0.112 AC XY: 8364 AN XY: 74386

African (AFR) AF: 0.376 AC: 15594 AN: 41434

American (AMR) AF: 0.0517 AC: 791 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0115 AC: 40 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5168

South Asian (SAS) AF: 0.0190 AC: 92 AN: 4834

European-Finnish (FIN) AF: 0.00170 AC: 18 AN: 10618

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.00978 AC: 665 AN: 68000

Other (OTH) AF: 0.0858 AC: 181 AN: 2110

Alfa AF: 0.0500 Hom.: 507

Bravo AF: 0.130

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6778854; hg19: chr3-588448;