rs786425

Variant names:

• chr12-123600955-G-A
• rs786425

Your query was ambiguous. Multiple possible variants found:

• chr12-123600955-G-A
• chr12-123600955-G-C
• chr12-123600955-G-T

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 0.462 in 152,090 control chromosomes in the GnomAD database, including 20,188 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 0.46 (20188 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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: 0.463 AC: 70315 AN: 151974 Hom.: 20185 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.462 AC: 70325 AN: 152090 Hom.: 20188 Cov.: 31 AF XY: 0.472 AC XY: 35119 AN XY: 74334

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.501

Alfa AF: 0.488 Hom.: 2645

Bravo AF: 0.445

Asia WGS AF: 0.664 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs786425; hg19: chr12-124085502;