rs16852244

Variant names:

• chr3-106275050-T-C
• rs16852244

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0281 in 152,288 control chromosomes in the GnomAD database, including 79 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 0.028 (79 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0281 (4273/152288) while in subpopulation AFR AF = 0.0513 (2131/41568). AF 95% confidence interval is 0.0495. There are 79 homozygotes in GnomAd4. There are 2141 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 79 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0279 AC: 4249 AN: 152170 Hom.: 79 Cov.: 31

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0281 AC: 4273 AN: 152288 Hom.: 79 Cov.: 31 AF XY: 0.0288 AC XY: 2141 AN XY: 74462

African (AFR) AF: 0.0513 AC: 2131 AN: 41568

American (AMR) AF: 0.0440 AC: 672 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.0456 AC: 236 AN: 5180

South Asian (SAS) AF: 0.0365 AC: 176 AN: 4826

European-Finnish (FIN) AF: 0.0162 AC: 172 AN: 10628

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0111 AC: 758 AN: 68014

Other (OTH) AF: 0.0317 AC: 67 AN: 2112

Alfa AF: 0.0266 Hom.: 11

Bravo AF: 0.0303

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16852244; hg19: chr3-105993897;