rs10506404

Variant names:

• chr12-60013812-T-C
• rs10506404

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 0.0397 in 151,820 control chromosomes in the GnomAD database, including 150 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 0.040 (150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.083 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: 0.0397 AC: 6018 AN: 151702 Hom.: 149 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00933

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0500

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

GnomAD4 genome AF: 0.0397 AC: 6027 AN: 151820 Hom.: 150 Cov.: 32 AF XY: 0.0392 AC XY: 2908 AN XY: 74210

Gnomad4 AFR AF: 0.0394

Gnomad4 AMR AF: 0.0869

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0531

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.00933

Gnomad4 NFE AF: 0.0358

Gnomad4 OTH AF: 0.0495

Alfa AF: 0.0378 Hom.: 21

Bravo AF: 0.0478

Asia WGS AF: 0.0290 AC: 102 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
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: rs10506404; hg19: chr12-60407593;