rs10875902

chr12-48961509-G-A

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 0.326 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.360

Alfa AF: 0.386 Hom.: 12594

Bravo AF: 0.337

Asia WGS AF: 0.363 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10875902; hg19: chr12-49355292;