3-19877852-C-G

Position:

• chr3-19877852-C-G

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 0.133 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.19877852C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0970

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0515

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.121

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
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: rs269384; hg19: chr3-19919344;