rs10500429

Variant names:

• chr16-60214238-C-T
• rs10500429

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 0.252 in 152,038 control chromosomes in the GnomAD database, including 5,287 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 0.25 (5287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.252 AC: 38245 AN: 151920 Hom.: 5277 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.252 AC: 38279 AN: 152038 Hom.: 5287 Cov.: 32 AF XY: 0.260 AC XY: 19303 AN XY: 74310

African (AFR) AF: 0.192 AC: 7969 AN: 41502

American (AMR) AF: 0.320 AC: 4887 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2760 AN: 5140

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4830

European-Finnish (FIN) AF: 0.292 AC: 3079 AN: 10538

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16002 AN: 67966

Other (OTH) AF: 0.286 AC: 603 AN: 2112

Alfa AF: 0.245 Hom.: 2440

Bravo AF: 0.251

Asia WGS AF: 0.427 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.86
DANN	Benign	0.68
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10500429; hg19: chr16-60248142;