rs10509096

Positions:

• chr10-59172315-G-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 0.0341 in 152,182 control chromosomes in the GnomAD database, including 233 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 0.034 (233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

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 (AFR) allele frequency at 95% confidence interval = 0.0968 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: 0.0339 AC: 5151 AN: 152064 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0987

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.000943

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00641

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0341 AC: 5187 AN: 152182 Hom.: 233 Cov.: 32 AF XY: 0.0327 AC XY: 2436 AN XY: 74410

Gnomad4 AFR AF: 0.0994

Gnomad4 AMR AF: 0.0295

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0191

Gnomad4 FIN AF: 0.000943

Gnomad4 NFE AF: 0.00641

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0212 Hom.: 14

Bravo AF: 0.0393

Asia WGS AF: 0.0270 AC: 94 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509096; hg19: chr10-60932075;