16-59895622-G-C

Variant names:

• chr16-59895622-G-C
• rs7198976
• ENST00000568279.2:n.173+40097G>C

Variant summary

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

The ENST00000568279.2(LINC02141):​n.173+40097G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,040 control chromosomes in the GnomAD database, including 8,261 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 0.26 (8261 hom., cov: 32)
• Consequence: LINC02141 ENST00000568279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 4 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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+40097G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02141	ENST00000568279.2	TSL:1	n.173+40097G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39520 AN: 151920 Hom.: 8233 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.260 AC: 39580 AN: 152040 Hom.: 8261 Cov.: 32 AF XY: 0.258 AC XY: 19173 AN XY: 74332

African (AFR) AF: 0.579 AC: 23978 AN: 41418

American (AMR) AF: 0.224 AC: 3418 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 543 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1557 AN: 5146

South Asian (SAS) AF: 0.236 AC: 1135 AN: 4814

European-Finnish (FIN) AF: 0.0600 AC: 636 AN: 10602

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7637 AN: 68004

Other (OTH) AF: 0.228 AC: 482 AN: 2114

Alfa AF: 0.0803 Hom.: 147

Bravo AF: 0.281

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.32
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7198976; hg19: chr16-59929526;