rs4888535

Variant names:

• chr16-76727759-T-A
• rs4888535
• ENST00000563764.2:n.*123-91827T>A

Your query was ambiguous. Multiple possible variants found:

• chr16-76727759-T-A
• chr16-76727759-T-C
• chr16-76727759-T-G

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-91827T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,886 control chromosomes in the GnomAD database, including 8,466 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 0.33 (8466 hom., cov: 32)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.902
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 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.*123-91827T>A		intron	N/A	ENSP00000455258.1	H3BPC8
	LINC02125	ENST00000567777.2	TSL:3	n.245-8558T>A		intron	N/A
	LINC02125	ENST00000751836.1		n.339-8558T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50069 AN: 151768 Hom.: 8464 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.330 AC: 50092 AN: 151886 Hom.: 8466 Cov.: 32 AF XY: 0.330 AC XY: 24511 AN XY: 74204

African (AFR) AF: 0.305 AC: 12640 AN: 41472

American (AMR) AF: 0.396 AC: 6038 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1186 AN: 3462

East Asian (EAS) AF: 0.381 AC: 1969 AN: 5166

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4814

European-Finnish (FIN) AF: 0.281 AC: 2972 AN: 10572

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22476 AN: 67848

Other (OTH) AF: 0.337 AC: 708 AN: 2104

Alfa AF: 0.331 Hom.: 1038

Bravo AF: 0.335

Asia WGS AF: 0.364 AC: 1258 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.79
PhyloP100		0.90

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: rs4888535;

hg19: chr16-76761656;