16-54547401-T-C

Variant names:

• chr16-54547401-T-C
• rs1211435
• ENST00000637822.1:n.225-1268A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000825114.1(LINC02183):​n.134-1911A>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 ENST00000825114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825114.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02183	ENST00000637822.1	TSL:5	n.225-1268A>G		intron	N/A
	LINC02183	ENST00000825114.1		n.134-1911A>G		intron	N/A

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

African (AFR) AF: 0.948 AC: 39342 AN: 41518

American (AMR) AF: 0.785 AC: 11996 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2723 AN: 3466

East Asian (EAS) AF: 0.796 AC: 4113 AN: 5164

South Asian (SAS) AF: 0.721 AC: 3471 AN: 4812

European-Finnish (FIN) AF: 0.676 AC: 7136 AN: 10564

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48523 AN: 67988

Other (OTH) AF: 0.809 AC: 1709 AN: 2112

Alfa AF: 0.752 Hom.: 80744

Bravo AF: 0.803

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.32
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1211435; hg19: chr16-54581313;