rs12725332

Variant names:

• chr1-103966390-G-A
• rs12725332

Your query was ambiguous. Multiple possible variants found:

• chr1-103966390-G-A
• chr1-103966390-G-C
• chr1-103966390-G-T

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 0.152 in 151,496 control chromosomes in the GnomAD database, including 2,139 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 (2139 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.152 AC: 23076 AN: 151380 Hom.: 2136 Cov.: 31

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.152 AC: 23074 AN: 151496 Hom.: 2139 Cov.: 31 AF XY: 0.153 AC XY: 11293 AN XY: 74002

African (AFR) AF: 0.0417 AC: 1723 AN: 41356

American (AMR) AF: 0.210 AC: 3200 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 279 AN: 3462

East Asian (EAS) AF: 0.236 AC: 1213 AN: 5136

South Asian (SAS) AF: 0.122 AC: 584 AN: 4784

European-Finnish (FIN) AF: 0.187 AC: 1945 AN: 10386

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13603 AN: 67804

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.179 Hom.: 8206

Bravo AF: 0.150

Asia WGS AF: 0.176 AC: 607 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.065
DANN	Benign	0.57
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs12725332; hg19: chr1-104509012;