rs2171168

Variant names:

• chr3-120852757-C-T
• rs2171168
• ENST00000658056.1:n.228-1848C>T

Variant summary

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

The ENST00000658056.1(ENSG00000287366):​n.228-1848C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,070 control chromosomes in the GnomAD database, including 8,002 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 0.31 (8002 hom., cov: 32)
• Consequence: ENSG00000287366 ENST00000658056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 3 publications found

Genes affected

ENSG00000287366 (HGNC:):

LINC02049 (HGNC:52889): (long intergenic non-protein coding RNA 2049)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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
ENSG00000287366	ENST00000658056.1	n.228-1848C>T		intron_variant	Intron 2 of 4
LINC02049	ENST00000661060.1	n.946+11803G>A		intron_variant	Intron 5 of 5
LINC02049	ENST00000720436.1	n.289+11803G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46920 AN: 151950 Hom.: 7990 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.309 AC: 46974 AN: 152070 Hom.: 8002 Cov.: 32 AF XY: 0.304 AC XY: 22621 AN XY: 74336

African (AFR) AF: 0.434 AC: 17995 AN: 41456

American (AMR) AF: 0.237 AC: 3620 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3470

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5180

South Asian (SAS) AF: 0.187 AC: 901 AN: 4828

European-Finnish (FIN) AF: 0.328 AC: 3468 AN: 10566

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18957 AN: 67982

Other (OTH) AF: 0.301 AC: 635 AN: 2108

Alfa AF: 0.285 Hom.: 1133

Bravo AF: 0.309

Asia WGS AF: 0.113 AC: 395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2171168; hg19: chr3-120571604; COSMIC: COSV69482919;