10-79900599-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 0.271 in 152,082 control chromosomes in the GnomAD database, including 6,830 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 0.27 (6830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.271 AC: 41133 AN: 151964 Hom.: 6828 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.271 AC: 41149 AN: 152082 Hom.: 6830 Cov.: 32 AF XY: 0.277 AC XY: 20563 AN XY: 74342

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.257

Alfa AF: 0.285 Hom.: 3596

Bravo AF: 0.255

Asia WGS AF: 0.530 AC: 1838 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.9
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2250992; hg19: chr10-81660355;