chr20-12456001-G-A

Variant names:

• chr20-12456001-G-A
• rs6078600

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 0.0894 in 152,096 control chromosomes in the GnomAD database, including 713 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 0.089 (713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13599 AN: 151978 Hom.: 713 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0773

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

GnomAD4 genome AF: 0.0894 AC: 13604 AN: 152096 Hom.: 713 Cov.: 32 AF XY: 0.0907 AC XY: 6746 AN XY: 74346

African (AFR) AF: 0.0431 AC: 1789 AN: 41536

American (AMR) AF: 0.120 AC: 1830 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3470

East Asian (EAS) AF: 0.136 AC: 700 AN: 5154

South Asian (SAS) AF: 0.132 AC: 636 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10582

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6989 AN: 67958

Other (OTH) AF: 0.0770 AC: 162 AN: 2104

Alfa AF: 0.0577 Hom.: 75

Bravo AF: 0.0872

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.1
DANN	Benign	0.49
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs6078600; hg19: chr20-12436649;