chr10-56937456-A-C

Position:

• chr10-56937456-A-C

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 0.107 in 152,172 control chromosomes in the GnomAD database, including 1,148 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 0.11 (1148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16200 AN: 152054 Hom.: 1144 Cov.: 32

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 16226 AN: 152172 Hom.: 1148 Cov.: 32 AF XY: 0.110 AC XY: 8199 AN XY: 74396

Gnomad4 AFR AF: 0.0570

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0925

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.0985

Gnomad4 OTH AF: 0.109

Alfa AF: 0.101 Hom.: 715

Bravo AF: 0.114

Asia WGS AF: 0.199 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12414237; hg19: chr10-58697216;