rs3924497

Variant names:

• chr16-76784266-C-T
• rs3924497
• ENST00000563764.2:n.*123-35320C>T

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-35320C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,010 control chromosomes in the GnomAD database, including 2,506 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 0.18 (2506 hom., cov: 32)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287694	ENST00000563764.2	n.*123-35320C>T		intron_variant	Intron 3 of 3	3		ENSP00000455258.1
LINC02125	ENST00000567777.2	n.407+47787C>T		intron_variant	Intron 3 of 4	3
LINC02125	ENST00000751836.1	n.501+47787C>T		intron_variant	Intron 3 of 4
LINC02125	ENST00000751837.1	n.326-46585C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27008 AN: 151894 Hom.: 2503 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.178 AC: 27013 AN: 152010 Hom.: 2506 Cov.: 32 AF XY: 0.176 AC XY: 13049 AN XY: 74300

African (AFR) AF: 0.168 AC: 6967 AN: 41490

American (AMR) AF: 0.157 AC: 2401 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1349 AN: 5138

South Asian (SAS) AF: 0.155 AC: 746 AN: 4810

European-Finnish (FIN) AF: 0.143 AC: 1509 AN: 10584

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12805 AN: 67946

Other (OTH) AF: 0.179 AC: 377 AN: 2110

Alfa AF: 0.179 Hom.: 646

Bravo AF: 0.177

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.65
PhyloP100		-0.13

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

Other links and lift over

dbSNP: rs3924497; hg19: chr16-76818163;