rs2331841

Variant names:

• chr18-60161404-G-A
• rs2331841
• ENST00000588794.1:n.*209G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-60161404-G-A
• chr18-60161404-G-C

Variant summary

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

The ENST00000588794.1(LINC03111):​n.*209G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,712 control chromosomes in the GnomAD database, including 14,598 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 0.43 (14598 hom., cov: 32)
• Consequence: LINC03111 ENST00000588794.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 32 publications found

Genes affected

LINC03111 (HGNC:56850): (long intergenic non-protein coding RNA 3111)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03111	NR_186639.1	n.*209G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03111	ENST00000588794.1	n.*209G>A		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65590 AN: 151594 Hom.: 14589 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.433 AC: 65632 AN: 151712 Hom.: 14598 Cov.: 32 AF XY: 0.430 AC XY: 31902 AN XY: 74124

African (AFR) AF: 0.489 AC: 20226 AN: 41368

American (AMR) AF: 0.347 AC: 5281 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3462

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5158

South Asian (SAS) AF: 0.519 AC: 2499 AN: 4818

European-Finnish (FIN) AF: 0.429 AC: 4505 AN: 10498

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29538 AN: 67864

Other (OTH) AF: 0.418 AC: 882 AN: 2112

Alfa AF: 0.433 Hom.: 34883

Bravo AF: 0.423

Asia WGS AF: 0.347 AC: 1202 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.82
DANN	Benign	0.48
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2331841; hg19: chr18-57828637;