rs2208921

Variant names:

• chr1-189711247-G-A
• rs2208921
• ENST00000758530.1:n.266-34266G>A

Variant summary

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

The ENST00000758530.1(LINC01701):​n.266-34266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,986 control chromosomes in the GnomAD database, including 15,941 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 0.45 (15941 hom., cov: 33)
• Consequence: LINC01701 ENST00000758530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 2 publications found

Genes affected

LINC01701 (HGNC:52489): (long intergenic non-protein coding RNA 1701)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01701	ENST00000758530.1	n.266-34266G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68777 AN: 151868 Hom.: 15932 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.453 AC: 68816 AN: 151986 Hom.: 15941 Cov.: 33 AF XY: 0.451 AC XY: 33464 AN XY: 74258

African (AFR) AF: 0.395 AC: 16369 AN: 41484

American (AMR) AF: 0.371 AC: 5678 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2354 AN: 5174

South Asian (SAS) AF: 0.410 AC: 1977 AN: 4818

European-Finnish (FIN) AF: 0.529 AC: 5573 AN: 10526

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33631 AN: 67922

Other (OTH) AF: 0.439 AC: 925 AN: 2108

Alfa AF: 0.452 Hom.: 2487

Bravo AF: 0.440

Asia WGS AF: 0.419 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.30
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2208921; hg19: chr1-189680377; COSMIC: COSV60003442;