12-48961509-G-A

Variant names:

• chr12-48961509-G-A
• rs10875902

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 0.326 in 152,086 control chromosomes in the GnomAD database, including 9,157 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 0.33 (9157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49575 AN: 151968 Hom.: 9148 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.326 AC: 49595 AN: 152086 Hom.: 9157 Cov.: 32 AF XY: 0.330 AC XY: 24527 AN XY: 74350

African (AFR) AF: 0.156 AC: 6488 AN: 41498

American (AMR) AF: 0.476 AC: 7272 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2410 AN: 5154

South Asian (SAS) AF: 0.219 AC: 1058 AN: 4822

European-Finnish (FIN) AF: 0.376 AC: 3972 AN: 10572

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25610 AN: 67980

Other (OTH) AF: 0.360 AC: 762 AN: 2114

Alfa AF: 0.378 Hom.: 19817

Bravo AF: 0.337

Asia WGS AF: 0.363 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.0
DANN	Benign	0.60
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs10875902; hg19: chr12-49355292;