3-627230-T-C

Variant summary

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

The NR_110118.1(LINC01266):n.79+35047T>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 0.159 in 151,996 control chromosomes in the GnomAD database, including 3,695 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 (3695 hom., cov: 32)
• Consequence: LINC01266 NR_110118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01266	NR_110118.1	n.79+35047T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01266	ENST00000661103.1	n.345+35047T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24039 AN: 151878 Hom.: 3673 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.159 AC: 24113 AN: 151996 Hom.: 3695 Cov.: 32 AF XY: 0.157 AC XY: 11635 AN XY: 74314

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.00368

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.0655

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0198 Hom.: 16

Bravo AF: 0.170

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.43
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9848984; hg19: chr3-668914;