ENST00000563764.2:n.*123-78565G>T

Variant names:

• chr16-76741021-G-T
• rs4337315
• ENST00000563764.2:n.*123-78565G>T

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-78565G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,948 control chromosomes in the GnomAD database, including 9,706 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 0.35 (9706 hom., cov: 32)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 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.*123-78565G>T		intron_variant	Intron 3 of 3	3		ENSP00000455258.1
LINC02125	ENST00000567777.2	n.407+4542G>T		intron_variant	Intron 3 of 4	3
LINC02125	ENST00000751836.1	n.501+4542G>T		intron_variant	Intron 3 of 4
LINC02125	ENST00000751837.1	n.325+4542G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53473 AN: 151828 Hom.: 9682 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.352 AC: 53537 AN: 151948 Hom.: 9706 Cov.: 32 AF XY: 0.352 AC XY: 26165 AN XY: 74256

African (AFR) AF: 0.395 AC: 16358 AN: 41446

American (AMR) AF: 0.404 AC: 6166 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1952 AN: 5148

South Asian (SAS) AF: 0.359 AC: 1727 AN: 4806

European-Finnish (FIN) AF: 0.278 AC: 2937 AN: 10548

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22127 AN: 67954

Other (OTH) AF: 0.353 AC: 745 AN: 2110

Alfa AF: 0.260 Hom.: 862

Bravo AF: 0.362

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.24
PhyloP100		-0.96

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: rs4337315; hg19: chr16-76774918;