20-56258375-C-A

Variant names:

• chr20-56258375-C-A
• rs6014657

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 0.199 in 152,078 control chromosomes in the GnomAD database, including 3,160 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 0.20 (3160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30315 AN: 151960 Hom.: 3160 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.199 AC: 30337 AN: 152078 Hom.: 3160 Cov.: 32 AF XY: 0.198 AC XY: 14747 AN XY: 74338

African (AFR) AF: 0.173 AC: 7165 AN: 41484

American (AMR) AF: 0.159 AC: 2431 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 887 AN: 3472

East Asian (EAS) AF: 0.101 AC: 526 AN: 5184

South Asian (SAS) AF: 0.180 AC: 866 AN: 4822

European-Finnish (FIN) AF: 0.219 AC: 2310 AN: 10540

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15506 AN: 67982

Other (OTH) AF: 0.198 AC: 419 AN: 2112

Alfa AF: 0.183 Hom.: 1115

Bravo AF: 0.193

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.36
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs6014657; hg19: chr20-54833431;