rs10506413

Variant names:

• chr12-60579893-G-C
• rs10506413

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 79 gene

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: 0.0265 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

African (AFR) AF: 0.00647 AC: 269 AN: 41552

American (AMR) AF: 0.0378 AC: 578 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3468

East Asian (EAS) AF: 0.00368 AC: 19 AN: 5170

South Asian (SAS) AF: 0.00311 AC: 15 AN: 4826

European-Finnish (FIN) AF: 0.0297 AC: 314 AN: 10588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2639 AN: 68002

Other (OTH) AF: 0.0270 AC: 57 AN: 2114

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10506413; hg19: chr12-60973674;