20-56238477-T-C

Variant names:

• chr20-56238477-T-C
• rs6024725

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 0.385 in 151,914 control chromosomes in the GnomAD database, including 12,152 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 0.38 (12152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.384 AC: 58358 AN: 151796 Hom.: 12132 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.385 AC: 58412 AN: 151914 Hom.: 12152 Cov.: 32 AF XY: 0.385 AC XY: 28564 AN XY: 74252

African (AFR) AF: 0.549 AC: 22700 AN: 41382

American (AMR) AF: 0.261 AC: 3990 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1444 AN: 3464

East Asian (EAS) AF: 0.290 AC: 1491 AN: 5146

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4818

European-Finnish (FIN) AF: 0.366 AC: 3865 AN: 10552

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.320 AC: 21759 AN: 67960

Other (OTH) AF: 0.355 AC: 750 AN: 2114

Alfa AF: 0.339 Hom.: 30873

Bravo AF: 0.382

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.77
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs6024725; hg19: chr20-54813533;