chr10-99856822-A-G

Position:

• chr10-99856822-A-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 0.326 in 152,182 control chromosomes in the GnomAD database, including 8,483 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 0.33 (8483 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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 (NFE) allele frequency at 95% confidence interval = 0.369 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: 0.326 AC: 49525 AN: 152064 Hom.: 8491 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.326 AC: 49538 AN: 152182 Hom.: 8483 Cov.: 33 AF XY: 0.324 AC XY: 24133 AN XY: 74382

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.345

Alfa AF: 0.365 Hom.: 21552

Bravo AF: 0.321

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7067971; hg19: chr10-101616579;