16-59906284-T-G

Variant names:

• chr16-59906284-T-G
• rs16961543
• ENST00000568279.2:n.173+50759T>G

Variant summary

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

The ENST00000568279.2(LINC02141):​n.173+50759T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,044 control chromosomes in the GnomAD database, including 10,049 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 (10049 hom., cov: 32)
• Consequence: LINC02141 ENST00000568279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568279.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02141	NR_110917.1		n.173+50759T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02141	ENST00000568279.2	TSL:1	n.173+50759T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46540 AN: 151926 Hom.: 10018 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.307 AC: 46614 AN: 152044 Hom.: 10049 Cov.: 32 AF XY: 0.303 AC XY: 22524 AN XY: 74338

African (AFR) AF: 0.617 AC: 25545 AN: 41418

American (AMR) AF: 0.258 AC: 3941 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5172

South Asian (SAS) AF: 0.274 AC: 1320 AN: 4826

European-Finnish (FIN) AF: 0.123 AC: 1302 AN: 10598

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11519 AN: 67976

Other (OTH) AF: 0.269 AC: 566 AN: 2106

Alfa AF: 0.221 Hom.: 15094

Bravo AF: 0.325

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs16961543; hg19: chr16-59940188;