rs999444

Variant names:

• chr12-113972623-G-A
• rs999444

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;