chr3-142945099-C-A

Variant names:

• chr3-142945099-C-A
• rs16852856

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 0.141 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0355 AC: 1475 AN: 41544

American (AMR) AF: 0.194 AC: 2966 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1563 AN: 5156

South Asian (SAS) AF: 0.168 AC: 810 AN: 4832

European-Finnish (FIN) AF: 0.296 AC: 3135 AN: 10582

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10556 AN: 67996

Other (OTH) AF: 0.133 AC: 281 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.80
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs16852856; hg19: chr3-142663941;