3-19877852-C-G

Variant names:

• chr3-19877852-C-G
• rs269384

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 0.133 in 151,496 control chromosomes in the GnomAD database, including 1,513 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 0.13 (1513 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

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: 0.134 AC: 20213 AN: 151378 Hom.: 1511 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0928

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.133 AC: 20221 AN: 151496 Hom.: 1513 Cov.: 31 AF XY: 0.131 AC XY: 9730 AN XY: 73998

African (AFR) AF: 0.182 AC: 7509 AN: 41208

American (AMR) AF: 0.0970 AC: 1472 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 642 AN: 3458

East Asian (EAS) AF: 0.0930 AC: 478 AN: 5140

South Asian (SAS) AF: 0.219 AC: 1050 AN: 4788

European-Finnish (FIN) AF: 0.0515 AC: 541 AN: 10508

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8028 AN: 67918

Other (OTH) AF: 0.121 AC: 255 AN: 2102

Alfa AF: 0.128 Hom.: 166

Bravo AF: 0.136

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs269384; hg19: chr3-19919344;