10-124389703-C-G

Position:

• chr10-124389703-C-G

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 0.282 in 151,982 control chromosomes in the GnomAD database, including 6,139 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 0.28 (6139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

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: 0.282 AC: 42806 AN: 151864 Hom.: 6133 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.282 AC: 42828 AN: 151982 Hom.: 6139 Cov.: 31 AF XY: 0.279 AC XY: 20710 AN XY: 74322

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.296

Alfa AF: 0.287 Hom.: 769

Bravo AF: 0.284

Asia WGS AF: 0.252 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11597880; hg19: chr10-126078272;