rs1447670

Variant names:

• chr3-186537043-A-G
• rs1447670

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 0.212 in 152,134 control chromosomes in the GnomAD database, including 4,072 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 0.21 (4072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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: 0.212 AC: 32267 AN: 152016 Hom.: 4064 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.212 AC: 32295 AN: 152134 Hom.: 4072 Cov.: 32 AF XY: 0.215 AC XY: 16005 AN XY: 74364

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.220

Alfa AF: 0.160 Hom.: 4439

Bravo AF: 0.217

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1447670; hg19: chr3-186254832;