rs8049365

Variant names:

• chr16-76785421-C-T
• rs8049365
• ENST00000563764.2:n.*123-34165C>T

Variant summary

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

The ENST00000563764.2(ENSG00000287694):​n.*123-34165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,042 control chromosomes in the GnomAD database, including 9,492 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 (9492 hom., cov: 33)
• Consequence: ENSG00000287694 ENST00000563764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287694	ENST00000563764.2	TSL:3	n.*123-34165C>T		intron	N/A	ENSP00000455258.1
	LINC02125	ENST00000567777.2	TSL:3	n.407+48942C>T		intron	N/A
	LINC02125	ENST00000751836.1		n.501+48942C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52935 AN: 151926 Hom.: 9475 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.421

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: 0.348 AC: 52985 AN: 152042 Hom.: 9492 Cov.: 33 AF XY: 0.349 AC XY: 25954 AN XY: 74314

African (AFR) AF: 0.381 AC: 15808 AN: 41484

American (AMR) AF: 0.403 AC: 6141 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1958 AN: 5156

South Asian (SAS) AF: 0.357 AC: 1722 AN: 4818

European-Finnish (FIN) AF: 0.279 AC: 2948 AN: 10584

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

European-Non Finnish (NFE) AF: 0.326 AC: 22128 AN: 67974

Other (OTH) AF: 0.352 AC: 743 AN: 2112

Alfa AF: 0.342 Hom.: 1530

Bravo AF: 0.357

Asia WGS AF: 0.374 AC: 1300 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	0.88
DANN	Benign	0.74
PhyloP100		-0.74

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: rs8049365; hg19: chr16-76819318;