rs10510197

Positions:

• chr3-681776-A-C

Variant summary

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

The NR_110118.1(LINC01266):​n.80-68439A>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 0.0399 in 151,876 control chromosomes in the GnomAD database, including 369 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 0.040 (369 hom., cov: 32)
• Consequence: LINC01266 NR_110118.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01266	NR_110118.1	n.80-68439A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01266	ENST00000661103.1	n.346-68439A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6036 AN: 151760 Hom.: 363 Cov.: 32

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.0336

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

GnomAD4 genome AF: 0.0399 AC: 6053 AN: 151876 Hom.: 369 Cov.: 32 AF XY: 0.0452 AC XY: 3356 AN XY: 74228

Gnomad4 AFR AF: 0.0222

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.0234

Gnomad4 OTH AF: 0.0375

Alfa AF: 0.0283 Hom.: 27

Bravo AF: 0.0352

Asia WGS AF: 0.208 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510197; hg19: chr3-723460;