rs16851

chr10-58313830-T-C

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 0.038 in 152,254 control chromosomes in the GnomAD database, including 202 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 0.038 (202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 5768 AN: 152136 Hom.: 202 Cov.: 32

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0380 AC: 5780 AN: 152254 Hom.: 202 Cov.: 32 AF XY: 0.0382 AC XY: 2841 AN XY: 74458

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.0204

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.00188

Gnomad4 NFE AF: 0.0185

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0272 Hom.: 21

Bravo AF: 0.0405

Asia WGS AF: 0.0350 AC: 121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	13
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16851; hg19: chr10-60073590;