3-172012066-A-G

Variant names:

• chr3-172012066-A-G
• rs567413

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 0.182 in 139,878 control chromosomes in the GnomAD database, including 2,855 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 0.18 (2855 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.182 AC: 25394 AN: 139838 Hom.: 2852 Cov.: 22

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0933

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.182 AC: 25398 AN: 139878 Hom.: 2855 Cov.: 22 AF XY: 0.176 AC XY: 11884 AN XY: 67650

African (AFR) AF: 0.301 AC: 11085 AN: 36840

American (AMR) AF: 0.147 AC: 2020 AN: 13758

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 574 AN: 3400

East Asian (EAS) AF: 0.0514 AC: 237 AN: 4614

South Asian (SAS) AF: 0.150 AC: 636 AN: 4238

European-Finnish (FIN) AF: 0.0933 AC: 814 AN: 8720

Middle Eastern (MID) AF: 0.165 AC: 47 AN: 284

European-Non Finnish (NFE) AF: 0.146 AC: 9545 AN: 65270

Other (OTH) AF: 0.168 AC: 313 AN: 1864

Alfa AF: 0.0834 Hom.: 132

Bravo AF: 0.187

Asia WGS AF: 0.108 AC: 374 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.091
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs567413; hg19: chr3-171729856;