10-99557320-A-G

Position:

• chr10-99557320-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 0.6 in 151,812 control chromosomes in the GnomAD database, including 28,052 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 0.60 (28052 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

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 = 0.728 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: 0.600 AC: 90983 AN: 151694 Hom.: 28011 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.600 AC: 91078 AN: 151812 Hom.: 28052 Cov.: 30 AF XY: 0.600 AC XY: 44540 AN XY: 74208

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.566

Alfa AF: 0.572 Hom.: 7911

Bravo AF: 0.611

Asia WGS AF: 0.590 AC: 2054 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	3.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332448; hg19: chr10-101317077;