16-59865225-T-G

Variant names:

• chr16-59865225-T-G
• rs1867612
• ENST00000568279.2:n.173+9700T>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+9700T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,180 control chromosomes in the GnomAD database, including 48,293 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 0.79 (48293 hom., cov: 33)
• Consequence: LINC02141 ENST00000568279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02141	NR_110917.1	n.173+9700T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02141	ENST00000568279.2	n.173+9700T>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120655 AN: 152062 Hom.: 48268 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.793 AC: 120727 AN: 152180 Hom.: 48293 Cov.: 33 AF XY: 0.788 AC XY: 58622 AN XY: 74398

African (AFR) AF: 0.697 AC: 28946 AN: 41510

American (AMR) AF: 0.870 AC: 13313 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3783 AN: 5166

South Asian (SAS) AF: 0.780 AC: 3758 AN: 4816

European-Finnish (FIN) AF: 0.745 AC: 7885 AN: 10590

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57321 AN: 68016

Other (OTH) AF: 0.809 AC: 1707 AN: 2110

Alfa AF: 0.816 Hom.: 31264

Bravo AF: 0.800

Asia WGS AF: 0.737 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1867612; hg19: chr16-59899129;