chr20-56273921-C-T

Variant names:

• chr20-56273921-C-T
• rs6014664

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 0.23 in 152,172 control chromosomes in the GnomAD database, including 4,188 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 0.23 (4188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 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: 0.230 AC: 34927 AN: 152054 Hom.: 4188 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.230 AC: 34961 AN: 152172 Hom.: 4188 Cov.: 32 AF XY: 0.228 AC XY: 16960 AN XY: 74406

African (AFR) AF: 0.237 AC: 9846 AN: 41524

American (AMR) AF: 0.175 AC: 2683 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3470

East Asian (EAS) AF: 0.138 AC: 715 AN: 5178

South Asian (SAS) AF: 0.193 AC: 930 AN: 4830

European-Finnish (FIN) AF: 0.224 AC: 2371 AN: 10600

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16668 AN: 67968

Other (OTH) AF: 0.239 AC: 504 AN: 2112

Alfa AF: 0.230 Hom.: 628

Bravo AF: 0.226

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.61
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6014664; hg19: chr20-54848977;