16-54547401-T-C

Position:

• chr16-54547401-T-C

Variant summary

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

The ENST00000637822.1(LINC02183):​n.225-1268A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,118 control chromosomes in the GnomAD database, including 48,032 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 (48032 hom., cov: 32)
• Consequence: LINC02183 ENST00000637822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

LINC02183 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02183	XR_933595.3	n.203-1268A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02183	ENST00000637822.1	n.225-1268A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119714 AN: 152002 Hom.: 47987 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.788 AC: 119815 AN: 152118 Hom.: 48032 Cov.: 32 AF XY: 0.786 AC XY: 58474 AN XY: 74356

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.809

Alfa AF: 0.730 Hom.: 41235

Bravo AF: 0.803

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
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: rs1211435; hg19: chr16-54581313;