rs4888543

Variant names:

• chr16-76764575-A-C
• rs4888543
• ENST00000563764.2:n.*123-55011A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-76764575-A-C
• chr16-76764575-A-T

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-55011A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,942 control chromosomes in the GnomAD database, including 10,458 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 0.36 (10458 hom., cov: 32)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 2 publications found

Genes affected

ENSG00000287694 (HGNC:):

LINC02125 (HGNC:52982): (long intergenic non-protein coding RNA 2125)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563764.2. 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
	ENSG00000287694	ENST00000563764.2	TSL:3	n.*123-55011A>C		intron	N/A	ENSP00000455258.1	H3BPC8
	LINC02125	ENST00000567777.2	TSL:3	n.407+28096A>C		intron	N/A
	LINC02125	ENST00000751836.1		n.501+28096A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55308 AN: 151822 Hom.: 10441 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.364 AC: 55359 AN: 151942 Hom.: 10458 Cov.: 32 AF XY: 0.364 AC XY: 27061 AN XY: 74254

African (AFR) AF: 0.435 AC: 18018 AN: 41422

American (AMR) AF: 0.409 AC: 6243 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1979 AN: 5164

South Asian (SAS) AF: 0.360 AC: 1731 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2952 AN: 10566

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22135 AN: 67928

Other (OTH) AF: 0.363 AC: 767 AN: 2112

Alfa AF: 0.273 Hom.: 985

Bravo AF: 0.375

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.7
DANN	Benign	0.16
PhyloP100		-0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4888543;

hg19: chr16-76798472;