chr16-60214238-C-T

Variant names:

• chr16-60214238-C-T
• rs10500429

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 0.252 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

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 (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

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.286

Alfa AF: 0.245 Hom.: 2190

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500429; hg19: chr16-60248142;