chr12-123600955-G-A

Position:

• chr12-123600955-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;