rs2216924

Variant names:

• chr2-66852811-C-A
• rs2216924
• ENST00000715601.1:n.276+4734C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-66852811-C-A
• chr2-66852811-C-G

Variant summary

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

The ENST00000715601.1(LINC01798):​n.276+4734C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,018 control chromosomes in the GnomAD database, including 5,989 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 0.28 (5989 hom., cov: 33)
• Consequence: LINC01798 ENST00000715601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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
LINC01798	ENST00000715601.1	n.276+4734C>A		intron_variant	Intron 3 of 6
LINC01798	ENST00000758432.1	n.276+4734C>A		intron_variant	Intron 3 of 5
LINC01798	ENST00000758436.1	n.338+4734C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42415 AN: 151898 Hom.: 5985 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.279 AC: 42457 AN: 152018 Hom.: 5989 Cov.: 33 AF XY: 0.279 AC XY: 20708 AN XY: 74278

African (AFR) AF: 0.247 AC: 10229 AN: 41448

American (AMR) AF: 0.253 AC: 3861 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1303 AN: 3464

East Asian (EAS) AF: 0.170 AC: 879 AN: 5178

South Asian (SAS) AF: 0.312 AC: 1500 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3342 AN: 10550

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20329 AN: 67964

Other (OTH) AF: 0.274 AC: 579 AN: 2112

Alfa AF: 0.284 Hom.: 1104

Bravo AF: 0.273

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.28
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2216924; hg19: chr2-67079943;