16-59906284-T-G

Position:

• chr16-59906284-T-G

Variant summary

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

The NR_110917.1(LINC02141):​n.173+50759T>G 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 0.307 in 152,044 control chromosomes in the GnomAD database, including 10,049 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 0.31 (10049 hom., cov: 32)
• Consequence: LINC02141 NR_110917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02141	NR_110917.1	n.173+50759T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02141	ENST00000568279.2	n.173+50759T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46540 AN: 151926 Hom.: 10018 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.307 AC: 46614 AN: 152044 Hom.: 10049 Cov.: 32 AF XY: 0.303 AC XY: 22524 AN XY: 74338

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.269

Alfa AF: 0.207 Hom.: 4785

Bravo AF: 0.325

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16961543; hg19: chr16-59940188;