rs999444

Positions:

• chr12-113972623-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 0.0855 in 152,218 control chromosomes in the GnomAD database, including 605 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 0.085 (605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.996

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 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: 0.0855 AC: 13006 AN: 152100 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.0855 AC: 13008 AN: 152218 Hom.: 605 Cov.: 32 AF XY: 0.0845 AC XY: 6284 AN XY: 74396

Gnomad4 AFR AF: 0.0547

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0976

Alfa AF: 0.0867 Hom.: 100

Bravo AF: 0.0837

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	17
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999444; hg19: chr12-114410428;