10-124103696-A-C

Position:

• chr10-124103696-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 0.704 in 152,154 control chromosomes in the GnomAD database, including 37,924 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 0.70 (37924 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.747 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: 0.705 AC: 107115 AN: 152036 Hom.: 37905 Cov.: 34

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.704 AC: 107183 AN: 152154 Hom.: 37924 Cov.: 34 AF XY: 0.704 AC XY: 52352 AN XY: 74390

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.724

Alfa AF: 0.722 Hom.: 31324

Bravo AF: 0.699

Asia WGS AF: 0.717 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7078615; hg19: chr10-125863212;