rs10082804

chr12-76246625-T-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 0.276 in 152,064 control chromosomes in the GnomAD database, including 8,381 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 0.28 (8381 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 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: 0.275 AC: 41855 AN: 151946 Hom.: 8346 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.276 AC: 41939 AN: 152064 Hom.: 8381 Cov.: 32 AF XY: 0.271 AC XY: 20169 AN XY: 74366

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.242

Alfa AF: 0.194 Hom.: 1793

Bravo AF: 0.288

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.89
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10082804; hg19: chr12-76640405;