16-59933662-A-G

Variant names:

• chr16-59933662-A-G
• rs1012273
• ENST00000568279.2:n.173+78137A>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+78137A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 150,154 control chromosomes in the GnomAD database, including 23,771 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 0.55 (23771 hom., cov: 29)
• Consequence: LINC02141 ENST00000568279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 1 publications found

Genes affected

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

LOC105371300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02141	NR_110917.1		n.173+78137A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02141	ENST00000568279.2	TSL:1	n.173+78137A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.546 AC: 81954 AN: 150032 Hom.: 23760 Cov.: 29

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.546 AC: 81997 AN: 150154 Hom.: 23771 Cov.: 29 AF XY: 0.536 AC XY: 39309 AN XY: 73278

African (AFR) AF: 0.368 AC: 14927 AN: 40520

American (AMR) AF: 0.578 AC: 8697 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2081 AN: 3448

East Asian (EAS) AF: 0.276 AC: 1416 AN: 5126

South Asian (SAS) AF: 0.396 AC: 1896 AN: 4782

European-Finnish (FIN) AF: 0.604 AC: 6289 AN: 10416

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.662 AC: 44721 AN: 67528

Other (OTH) AF: 0.547 AC: 1142 AN: 2086

Alfa AF: 0.634 Hom.: 31806

Bravo AF: 0.541

Asia WGS AF: 0.345 AC: 1197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1012273; hg19: chr16-59967566;