rs7964864

Variant names:

• chr12-74296512-A-C
• rs7964864
• ENST00000551726.2:n.464+10046T>G

Variant summary

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

The ENST00000551726.2(LINC02882):​n.464+10046T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,240 control chromosomes in the GnomAD database, including 1,047 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 0.11 (1047 hom., cov: 33)
• Consequence: LINC02882 ENST00000551726.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

LINC02882 (HGNC:54802): (long intergenic non-protein coding RNA 2882)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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
LINC02882	ENST00000551726.2	n.464+10046T>G		intron_variant	Intron 4 of 6	4
LINC02882	ENST00000653134.1	n.477+10046T>G		intron_variant	Intron 4 of 8
LINC02882	ENST00000656876.1	n.416+10046T>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16352 AN: 152122 Hom.: 1048 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0761

Gnomad ASJ AF: 0.0981

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.107 AC: 16358 AN: 152240 Hom.: 1047 Cov.: 33 AF XY: 0.108 AC XY: 8043 AN XY: 74440

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0760

Gnomad4 ASJ AF: 0.0981

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0712

Gnomad4 NFE AF: 0.0767

Gnomad4 OTH AF: 0.0966

Alfa AF: 0.0822 Hom.: 774

Bravo AF: 0.109

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7964864; hg19: chr12-74690292;