rs4671761

chr2-66945809-T-C

Variant summary

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

The NR_110169.1(LINC01799):n.438+335T>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 0.231 in 152,038 control chromosomes in the GnomAD database, including 4,514 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 (4514 hom., cov: 33)
• Consequence: LINC01799 NR_110169.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941

Genes affected

LINC01799 (HGNC:52589): (long intergenic non-protein coding RNA 1799)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01799	NR_110169.1	n.438+335T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01799	ENST00000426260.5	n.438+335T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35140 AN: 151920 Hom.: 4515 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.231 AC: 35140 AN: 152038 Hom.: 4514 Cov.: 33 AF XY: 0.232 AC XY: 17230 AN XY: 74312

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.267

Alfa AF: 0.271 Hom.: 7949

Bravo AF: 0.232

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4671761; hg19: chr2-67172941;