16-59865225-T-G

Position:

• chr16-59865225-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+9700T>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 0.793 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 NR_110917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641

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=-0.79).
• 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/exons	MANE	UniProt
LINC02141	NR_110917.1	n.173+9700T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02141	ENST00000568279.2	n.173+9700T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.809

Alfa AF: 0.819 Hom.: 20692

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1867612; hg19: chr16-59899129;