rs16852856

Variant names:

• chr3-142945099-C-A
• rs16852856

Your query was ambiguous. Multiple possible variants found:

• chr3-142945099-C-A
• chr3-142945099-C-G
• chr3-142945099-C-T

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 0.141 in 152,176 control chromosomes in the GnomAD database, including 1,927 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 0.14 (1927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 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: 0.141 AC: 21480 AN: 152058 Hom.: 1926 Cov.: 32

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.141 AC: 21492 AN: 152176 Hom.: 1927 Cov.: 32 AF XY: 0.150 AC XY: 11183 AN XY: 74384

Gnomad4 AFR AF: 0.0355

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0987 Hom.: 230

Bravo AF: 0.130

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16852856; hg19: chr3-142663941;