rs10506413

chr12-60579893-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0265 in 152,202 control chromosomes in the GnomAD database, including 79 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 0.026 (79 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0265 (4033/152202) while in subpopulation NFE AF= 0.0388 (2639/68002). AF 95% confidence interval is 0.0376. There are 79 homozygotes in gnomad4. There are 1896 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 79 gene

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: 0.0265 AC: 4034 AN: 152084 Hom.: 79 Cov.: 32

Gnomad AFR AF: 0.00649

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.0297

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0265 AC: 4033 AN: 152202 Hom.: 79 Cov.: 32 AF XY: 0.0255 AC XY: 1896 AN XY: 74420

Gnomad4 AFR AF: 0.00647

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.00368

Gnomad4 SAS AF: 0.00311

Gnomad4 FIN AF: 0.0297

Gnomad4 NFE AF: 0.0388

Gnomad4 OTH AF: 0.0270

Alfa AF: 0.0338 Hom.: 19

Bravo AF: 0.0275

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.94
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506413; hg19: chr12-60973674;