rs16953659

Positions:

• chr16-54553520-A-G
• chr16-54553520-A-T

Variant summary

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

The ENST00000637822.1(LINC02183):​n.224+2487T>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 0.0448 in 152,340 control chromosomes in the GnomAD database, including 208 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 0.045 (208 hom., cov: 33)
• Consequence: LINC02183 ENST00000637822.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

LINC02183 (HGNC:53045): (long intergenic non-protein coding RNA 2183)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02183	XR_933595.3	n.202+2487T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02183	ENST00000637822.1	n.224+2487T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0447 AC: 6810 AN: 152222 Hom.: 209 Cov.: 33

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0282

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0448 AC: 6819 AN: 152340 Hom.: 208 Cov.: 33 AF XY: 0.0418 AC XY: 3117 AN XY: 74500

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.0282

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0329

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0308 Hom.: 87

Bravo AF: 0.0481

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16953659; hg19: chr16-54587432;