rs12479885

chr20-31398024-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 0.0826 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

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 (NFE) allele frequency at 95% confidence interval = 0.104 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: 0.0826 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

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0525

Gnomad4 SAS AF: 0.0612

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0915

Alfa AF: 0.107 Hom.: 1337

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12479885; hg19: chr20-29985827;