3-184112605-G-A

Position:

• chr3-184112605-G-A

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 0.139 in 152,178 control chromosomes in the GnomAD database, including 1,716 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 (1716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21190 AN: 152060 Hom.: 1717 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.139 AC: 21203 AN: 152178 Hom.: 1716 Cov.: 32 AF XY: 0.137 AC XY: 10190 AN XY: 74410

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0328

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.141

Alfa AF: 0.179 Hom.: 2759

Bravo AF: 0.132

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11718245; hg19: chr3-183830393;