10-113944699-C-A

Position:

• chr10-113944699-C-A

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 0.0652 in 152,182 control chromosomes in the GnomAD database, including 427 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 0.065 (427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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: 0.0652 AC: 9907 AN: 152064 Hom.: 423 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0270

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0652 AC: 9929 AN: 152182 Hom.: 427 Cov.: 32 AF XY: 0.0651 AC XY: 4844 AN XY: 74390

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.0457

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0451 Hom.: 254

Bravo AF: 0.0642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7894582; hg19: chr10-115704458;