rs12479885

Variant names:

• chr20-31398024-C-T
• rs12479885

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0826 in 151,636 control chromosomes in the GnomAD database, including 602 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 0.083 (602 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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: 0.0826 AC: 12522 AN: 151516 Hom.: 603 Cov.: 31

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0826 AC: 12518 AN: 151636 Hom.: 602 Cov.: 31 AF XY: 0.0802 AC XY: 5942 AN XY: 74094

African (AFR) AF: 0.0506 AC: 2092 AN: 41354

American (AMR) AF: 0.0693 AC: 1053 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3466

East Asian (EAS) AF: 0.0525 AC: 270 AN: 5142

South Asian (SAS) AF: 0.0612 AC: 293 AN: 4788

European-Finnish (FIN) AF: 0.0736 AC: 771 AN: 10470

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7181 AN: 67916

Other (OTH) AF: 0.0915 AC: 192 AN: 2098

Alfa AF: 0.106 Hom.: 1704

Bravo AF: 0.0817

Asia WGS AF: 0.0440 AC: 153 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	4.6
DANN	Benign	0.55
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs12479885; hg19: chr20-29985827;