rs10500530

Variant names:

• chr16-65881602-G-A
• rs10500530

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0692 AC: 2875 AN: 41530

American (AMR) AF: 0.0766 AC: 1171 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1162 AN: 5168

South Asian (SAS) AF: 0.115 AC: 555 AN: 4808

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0146 AC: 991 AN: 68008

Other (OTH) AF: 0.0545 AC: 115 AN: 2112

Alfa AF: 0.0349 Hom.: 23

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10500530; hg19: chr16-65915505;