rs10505459

Variant names:

• chr8-125826623-G-A
• rs10505459
• ENST00000651999.1:n.353-60215G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651999.1(LINC02964):​n.353-60215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 152,054 control chromosomes in the GnomAD database, including 1,228 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 0.078 (1228 hom., cov: 32)
• Consequence: LINC02964 ENST00000651999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.231 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
LINC02964	ENST00000651999.1	n.353-60215G>A		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11828 AN: 151936 Hom.: 1214 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0521

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00622

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0781 AC: 11883 AN: 152054 Hom.: 1228 Cov.: 32 AF XY: 0.0781 AC XY: 5807 AN XY: 74324

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.0520

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.0300

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.00622

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.0486 Hom.: 82

Bravo AF: 0.0864

Asia WGS AF: 0.119 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505459; hg19: chr8-126838867;