rs10509210

chr10-64695553-C-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 0.0284 in 151,714 control chromosomes in the GnomAD database, including 143 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 0.028 (143 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

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 = 0.144 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: 0.0283 AC: 4290 AN: 151596 Hom.: 143 Cov.: 31

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0148

Gnomad ASJ AF: 0.00347

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00377

Gnomad OTH AF: 0.0197

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

GnomAD4 genome AF: 0.0284 AC: 4304 AN: 151714 Hom.: 143 Cov.: 31 AF XY: 0.0308 AC XY: 2280 AN XY: 74138

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.00347

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.0380

Gnomad4 NFE AF: 0.00378

Gnomad4 OTH AF: 0.0229

Alfa AF: 0.0171 Hom.: 9

Bravo AF: 0.0280

Asia WGS AF: 0.0980 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.93
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509210; hg19: chr10-66455310;