12-47969470-C-G

Variant names:

• chr12-47969470-C-G
• rs10875712

Variant summary

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

The variant allele was found at a frequency of 0.704 in 152,126 control chromosomes in the GnomAD database, including 38,456 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 0.70 (38456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106961 AN: 152008 Hom.: 38407 Cov.: 33

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.704 AC: 107063 AN: 152126 Hom.: 38456 Cov.: 33 AF XY: 0.703 AC XY: 52251 AN XY: 74376

African (AFR) AF: 0.819 AC: 34001 AN: 41510

American (AMR) AF: 0.734 AC: 11201 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2058 AN: 3466

East Asian (EAS) AF: 0.979 AC: 5075 AN: 5186

South Asian (SAS) AF: 0.730 AC: 3518 AN: 4818

European-Finnish (FIN) AF: 0.555 AC: 5866 AN: 10578

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 43114 AN: 67982

Other (OTH) AF: 0.703 AC: 1486 AN: 2114

Alfa AF: 0.668 Hom.: 4264

Bravo AF: 0.722

Asia WGS AF: 0.824 AC: 2862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.55
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10875712; hg19: chr12-48363253;