rs1002486

Positions:

• chr3-34581429-A-C
• chr3-34581429-A-G
• chr3-34581429-A-T

Variant summary

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

The ENST00000659779.1(LINC01811):​n.379-86708A>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 0.233 in 151,586 control chromosomes in the GnomAD database, including 5,127 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 0.23 (5127 hom., cov: 32)
• Consequence: LINC01811 ENST00000659779.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576

Genes affected

LINC01811 (HGNC:52615): (long intergenic non-protein coding RNA 1811)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01811	ENST00000659779.1	n.379-86708A>C		intron_variant, non_coding_transcript_variant
LINC01811	ENST00000669904.1	n.240-86708A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35291 AN: 151468 Hom.: 5120 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.233 AC: 35328 AN: 151586 Hom.: 5127 Cov.: 32 AF XY: 0.237 AC XY: 17553 AN XY: 74060

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.0812

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.212

Alfa AF: 0.158 Hom.: 3116

Bravo AF: 0.252

Asia WGS AF: 0.276 AC: 957 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1002486; hg19: chr3-34622921; COSMIC: COSV70043780;