rs4671761

Variant names:

• chr2-66945809-T-C
• rs4671761
• ENST00000411701.1:n.253+335T>C

Variant summary

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

The ENST00000411701.1(LINC01798):​n.253+335T>C variant causes a intron 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: LINC01798 ENST00000411701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941
• Publications: 4 publications found

Genes affected

LINC01798 (HGNC:52588): (long intergenic non-protein coding RNA 1798)

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411701.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01799	NR_110169.1		n.438+335T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01798	ENST00000411701.1	TSL:3	n.253+335T>C		intron	N/A
	LINC01798	ENST00000426260.5	TSL:3	n.438+335T>C		intron	N/A
	LINC01798	ENST00000657974.1		n.357+335T>C		intron	N/A

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

African (AFR) AF: 0.113 AC: 4678 AN: 41520

American (AMR) AF: 0.274 AC: 4183 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2054 AN: 5140

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4828

European-Finnish (FIN) AF: 0.243 AC: 2573 AN: 10578

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18545 AN: 67924

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.266 Hom.: 9539

Bravo AF: 0.232

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs4671761; hg19: chr2-67172941;