16-59856794-G-A

Position:

• chr16-59856794-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110917.1(LINC02141):​n.173+1269G>A variant causes a intron, non coding transcript 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 NR_110917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02141	NR_110917.1	n.173+1269G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02141	ENST00000568279.2	n.173+1269G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0837

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0784

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0873 Hom.: 1053

Bravo AF: 0.134

Asia WGS AF: 0.169 AC: 588 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8056650; hg19: chr16-59890698;