rs10509210

Variant names:

• chr10-64695553-C-G
• rs10509210

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;