chr10-56928856-G-C

Variant names:

• chr10-56928856-G-C
• rs16909785

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 151,964 control chromosomes in the GnomAD database, including 1,155 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 (1155 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=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16179 AN: 151846 Hom.: 1151 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.107 AC: 16205 AN: 151964 Hom.: 1155 Cov.: 32 AF XY: 0.110 AC XY: 8181 AN XY: 74272

Gnomad4 AFR AF: 0.0570

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.0985

Gnomad4 OTH AF: 0.108

Alfa AF: 0.102 Hom.: 122

Bravo AF: 0.113

Asia WGS AF: 0.197 AC: 686 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16909785; hg19: chr10-58688616;