20-48622896-G-C

Variant names:

• chr20-48622896-G-C
• rs6012501

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 0.41 in 152,050 control chromosomes in the GnomAD database, including 12,937 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 0.41 (12937 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 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: 0.410 AC: 62293 AN: 151934 Hom.: 12917 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.410 AC: 62359 AN: 152050 Hom.: 12937 Cov.: 32 AF XY: 0.407 AC XY: 30264 AN XY: 74310

African (AFR) AF: 0.407 AC: 16879 AN: 41442

American (AMR) AF: 0.451 AC: 6893 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1545 AN: 3472

East Asian (EAS) AF: 0.346 AC: 1789 AN: 5172

South Asian (SAS) AF: 0.522 AC: 2512 AN: 4812

European-Finnish (FIN) AF: 0.343 AC: 3631 AN: 10572

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.407 AC: 27654 AN: 67986

Other (OTH) AF: 0.431 AC: 912 AN: 2114

Alfa AF: 0.389 Hom.: 1457

Bravo AF: 0.415

Asia WGS AF: 0.425 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.67
DANN	Benign	0.76
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6012501; hg19: chr20-47239434;