rs16851260

chr3-162676031-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 0.187 in 152,148 control chromosomes in the GnomAD database, including 2,958 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 0.19 (2958 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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: 0.187 AC: 28402 AN: 152030 Hom.: 2949 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.187 AC: 28451 AN: 152148 Hom.: 2958 Cov.: 33 AF XY: 0.188 AC XY: 13975 AN XY: 74386

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.157

Alfa AF: 0.178 Hom.: 420

Bravo AF: 0.190

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	13
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16851260; hg19: chr3-162393819;