rs725063

Variant names:

• chr12-30309145-G-A
• rs725063

Your query was ambiguous. Multiple possible variants found:

• chr12-30309145-G-A
• chr12-30309145-G-C

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 0.256 in 150,074 control chromosomes in the GnomAD database, including 6,258 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 0.26 (6258 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 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: 0.256 AC: 38386 AN: 150016 Hom.: 6261 Cov.: 30

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.00934

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.256 AC: 38378 AN: 150074 Hom.: 6258 Cov.: 30 AF XY: 0.252 AC XY: 18447 AN XY: 73196

Gnomad4 AFR AF: 0.0752

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.00936

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.268

Alfa AF: 0.309 Hom.: 997

Bravo AF: 0.240

Asia WGS AF: 0.0900 AC: 313 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725063; hg19: chr12-30462078;