chr8-125635890-T-C

Variant names:

• chr8-125635890-T-C
• rs2124036
• XR_001746072.2:n.1927+12316T>C

Variant summary

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

The XR_001746072.2(LINC02964):​n.1927+12316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,640 control chromosomes in the GnomAD database, including 17,249 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 0.41 (17249 hom., cov: 30)
• Consequence: LINC02964 XR_001746072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 9 publications found

Genes affected

LINC02964 (HGNC:53487): (long intergenic non-protein coding RNA 2964)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.409 AC: 61929 AN: 151526 Hom.: 17201 Cov.: 30

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.409 AC: 62036 AN: 151640 Hom.: 17249 Cov.: 30 AF XY: 0.407 AC XY: 30158 AN XY: 74068

African (AFR) AF: 0.787 AC: 32490 AN: 41278

American (AMR) AF: 0.404 AC: 6138 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2470 AN: 5148

South Asian (SAS) AF: 0.374 AC: 1795 AN: 4798

European-Finnish (FIN) AF: 0.212 AC: 2227 AN: 10520

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.223 AC: 15162 AN: 67920

Other (OTH) AF: 0.378 AC: 791 AN: 2092

Alfa AF: 0.276 Hom.: 12049

Bravo AF: 0.442

Asia WGS AF: 0.462 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2124036; hg19: chr8-126648134;