rs2194198

Variant names:

• chr19-31545785-G-A
• rs2194198
• ENST00000593063.2:n.283-2723G>A

Variant summary

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

The ENST00000593063.2(LINC02841):​n.283-2723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,146 control chromosomes in the GnomAD database, including 6,304 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 (6304 hom., cov: 32)
• Consequence: LINC02841 ENST00000593063.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 2 publications found

Genes affected

LINC02841 (HGNC:54376): (long intergenic non-protein coding RNA 2841)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593063.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02841	NR_184026.1		n.139-2723G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02841	ENST00000593063.2	TSL:4	n.283-2723G>A		intron	N/A
	LINC02841	ENST00000664841.2		n.192-2723G>A		intron	N/A
	LINC02841	ENST00000842796.1		n.171-2723G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42347 AN: 152028 Hom.: 6308 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.278 AC: 42355 AN: 152146 Hom.: 6304 Cov.: 32 AF XY: 0.273 AC XY: 20281 AN XY: 74388

African (AFR) AF: 0.231 AC: 9598 AN: 41498

American (AMR) AF: 0.220 AC: 3368 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1396 AN: 3466

East Asian (EAS) AF: 0.0522 AC: 270 AN: 5168

South Asian (SAS) AF: 0.264 AC: 1273 AN: 4826

European-Finnish (FIN) AF: 0.283 AC: 3004 AN: 10600

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22416 AN: 67974

Other (OTH) AF: 0.290 AC: 611 AN: 2108

Alfa AF: 0.315 Hom.: 16453

Bravo AF: 0.269

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.027
DANN	Benign	0.34
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2194198; hg19: chr19-32036691;