chr10-59172315-G-A

Variant names:

• chr10-59172315-G-A
• rs10509096

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;