rs722919

chr12-63384174-C-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 0.154 in 151,892 control chromosomes in the GnomAD database, including 2,163 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 (2163 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 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: 0.154 AC: 23342 AN: 151774 Hom.: 2151 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0445

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.154 AC: 23396 AN: 151892 Hom.: 2163 Cov.: 31 AF XY: 0.160 AC XY: 11838 AN XY: 74218

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.0445

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.145

Alfa AF: 0.112 Hom.: 2393

Bravo AF: 0.158

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.23
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722919; hg19: chr12-63777954;