rs10500530

Variant names:

• chr16-65881602-G-A
• rs10500530

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 0.0483 in 152,208 control chromosomes in the GnomAD database, including 317 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 0.048 (317 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 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: 0.0482 AC: 7338 AN: 152090 Hom.: 319 Cov.: 33

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0483 AC: 7346 AN: 152208 Hom.: 317 Cov.: 33 AF XY: 0.0523 AC XY: 3888 AN XY: 74398

Gnomad4 AFR AF: 0.0692

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0146

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0327 Hom.: 19

Bravo AF: 0.0513

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500530; hg19: chr16-65915505;