rs10500999

Variant names:

• chr11-25188016-T-C
• rs10500999

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 0.0263 in 151,940 control chromosomes in the GnomAD database, including 87 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 0.026 (87 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.058 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: 0.0263 AC: 3987 AN: 151822 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0263 AC: 4000 AN: 151940 Hom.: 87 Cov.: 32 AF XY: 0.0267 AC XY: 1986 AN XY: 74260

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.0179

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0133

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.0176 Hom.: 8

Bravo AF: 0.0261

Asia WGS AF: 0.0110 AC: 37 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500999; hg19: chr11-25209562;