rs7964864

Variant names:

• chr12-74296512-A-C
• rs7964864
• ENST00000548427.2:n.1128-3438T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551726.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02882	ENST00000548427.2	TSL:6	n.1128-3438T>G		intron	N/A
	LINC02882	ENST00000551726.2	TSL:4	n.464+10046T>G		intron	N/A
	LINC02882	ENST00000653134.1		n.477+10046T>G		intron	N/A

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

African (AFR) AF: 0.177 AC: 7369 AN: 41526

American (AMR) AF: 0.0760 AC: 1162 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0981 AC: 340 AN: 3466

East Asian (EAS) AF: 0.0973 AC: 505 AN: 5188

South Asian (SAS) AF: 0.147 AC: 712 AN: 4834

European-Finnish (FIN) AF: 0.0712 AC: 756 AN: 10614

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0767 AC: 5215 AN: 67996

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.0846 Hom.: 1059

Bravo AF: 0.109

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.68
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7964864; hg19: chr12-74690292;