chr16-59856794-G-A

Variant names:

• chr16-59856794-G-A
• rs8056650
• ENST00000568279.2:n.173+1269G>A

Variant summary

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

The ENST00000568279.2(LINC02141):​n.173+1269G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,046 control chromosomes in the GnomAD database, including 1,509 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 0.13 (1509 hom., cov: 32)
• Consequence: LINC02141 ENST00000568279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 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+1269G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02141	ENST00000568279.2	TSL:1	n.173+1269G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19414 AN: 151928 Hom.: 1502 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0837

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.128 AC: 19436 AN: 152046 Hom.: 1509 Cov.: 32 AF XY: 0.130 AC XY: 9665 AN XY: 74296

African (AFR) AF: 0.198 AC: 8224 AN: 41486

American (AMR) AF: 0.147 AC: 2238 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0837 AC: 290 AN: 3466

East Asian (EAS) AF: 0.257 AC: 1318 AN: 5136

South Asian (SAS) AF: 0.119 AC: 573 AN: 4832

European-Finnish (FIN) AF: 0.108 AC: 1140 AN: 10574

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0784 AC: 5334 AN: 67994

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.0958 Hom.: 3101

Bravo AF: 0.134

Asia WGS AF: 0.169 AC: 588 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs8056650; hg19: chr16-59890698;