chr3-172524100-G-A

Variant names:

• chr3-172524100-G-A
• rs12488654

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 0.162 in 152,208 control chromosomes in the GnomAD database, including 2,748 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 0.16 (2748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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: 0.162 AC: 24661 AN: 152090 Hom.: 2750 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.162 AC: 24665 AN: 152208 Hom.: 2748 Cov.: 32 AF XY: 0.168 AC XY: 12519 AN XY: 74402

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.166

Alfa AF: 0.159 Hom.: 310

Bravo AF: 0.151

Asia WGS AF: 0.434 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12488654; hg19: chr3-172241890;