16-59895622-G-C

Position:

• chr16-59895622-G-C

Variant summary

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

The NR_110917.1(LINC02141):​n.173+40097G>C 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 0.26 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 NR_110917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02141	NR_110917.1	n.173+40097G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02141	ENST00000568279.2	n.173+40097G>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.228

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7198976; hg19: chr16-59929526;