chr3-187825554-A-G

Position:

• chr3-187825554-A-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 0.124 in 152,264 control chromosomes in the GnomAD database, including 1,371 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 0.12 (1371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18796 AN: 152146 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.124 AC: 18806 AN: 152264 Hom.: 1371 Cov.: 32 AF XY: 0.123 AC XY: 9131 AN XY: 74450

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.143

Alfa AF: 0.124 Hom.: 187

Bravo AF: 0.128

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
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: rs10513821; hg19: chr3-187543342;