rs768462

Variant names:

• chr16-60035944-C-A
• rs768462
• ENST00000568279.2:n.174-8767C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-60035944-C-A
• chr16-60035944-C-G
• chr16-60035944-C-T

Variant summary

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

The ENST00000568279.2(LINC02141):​n.174-8767C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,046 control chromosomes in the GnomAD database, including 6,442 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 (6442 hom., cov: 32)
• Consequence: LINC02141 ENST00000568279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 2 publications found

Genes affected

LINC02141 (HGNC:53001): (long intergenic non-protein coding RNA 2141)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02141	NR_110917.1	n.174-8767C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02141	ENST00000568279.2	n.174-8767C>A		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42590 AN: 151928 Hom.: 6441 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.280 AC: 42592 AN: 152046 Hom.: 6442 Cov.: 32 AF XY: 0.287 AC XY: 21341 AN XY: 74296

African (AFR) AF: 0.178 AC: 7377 AN: 41470

American (AMR) AF: 0.283 AC: 4313 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2746 AN: 5170

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4822

European-Finnish (FIN) AF: 0.358 AC: 3786 AN: 10568

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20498 AN: 67980

Other (OTH) AF: 0.303 AC: 640 AN: 2114

Alfa AF: 0.288 Hom.: 2242

Bravo AF: 0.269

Asia WGS AF: 0.446 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs768462; hg19: chr16-60069848;