12-63051312-G-A

Variant names:

• chr12-63051312-G-A
• rs10506458

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 0.0988 in 152,176 control chromosomes in the GnomAD database, including 866 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 0.099 (866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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 (EAS) allele frequency at 95% confidence interval = 0.171 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: 0.0989 AC: 15033 AN: 152058 Hom.: 866 Cov.: 32

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.0988 AC: 15037 AN: 152176 Hom.: 866 Cov.: 32 AF XY: 0.0996 AC XY: 7412 AN XY: 74392

Gnomad4 AFR AF: 0.0487

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0926

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0995 Hom.: 595

Bravo AF: 0.102

Asia WGS AF: 0.145 AC: 503 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	0.82
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506458; hg19: chr12-63445092;