3-152112520-A-G

Variant names:

• chr3-152112520-A-G
• rs11712066

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 0.15 in 152,118 control chromosomes in the GnomAD database, including 2,304 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 0.15 (2304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22758 AN: 152000 Hom.: 2306 Cov.: 32

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.150 AC: 22756 AN: 152118 Hom.: 2304 Cov.: 32 AF XY: 0.146 AC XY: 10819 AN XY: 74346

Gnomad4 AFR AF: 0.0405

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0951

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.158

Alfa AF: 0.197 Hom.: 4409

Bravo AF: 0.139

Asia WGS AF: 0.0500 AC: 174 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11712066; hg19: chr3-151830309;