rs7964864

Positions:

• chr12-74296512-A-C

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.74296512A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02882	ENST00000551726.2	n.464+10046T>G		intron_variant		4
LINC02882	ENST00000653134.1	n.477+10046T>G		intron_variant
LINC02882	ENST00000656876.1	n.416+10046T>G		intron_variant

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;