chr10-20385724-A-G

Variant names:

• chr10-20385724-A-G
• rs12772794

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 0.356 in 152,116 control chromosomes in the GnomAD database, including 11,088 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 0.36 (11088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

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 (EAS) allele frequency at 95% confidence interval = 0.538 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: 0.356 AC: 54151 AN: 151998 Hom.: 11088 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.356 AC: 54152 AN: 152116 Hom.: 11088 Cov.: 32 AF XY: 0.361 AC XY: 26872 AN XY: 74354

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.358

Alfa AF: 0.420 Hom.: 24026

Bravo AF: 0.344

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12772794; hg19: chr10-20674653;