chr20-25117290-G-C

Variant names:

• chr20-25117290-G-C
• rs6050337

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 0.384 in 152,042 control chromosomes in the GnomAD database, including 14,529 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 (14529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58216 AN: 151924 Hom.: 14492 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.384 AC: 58315 AN: 152042 Hom.: 14529 Cov.: 32 AF XY: 0.379 AC XY: 28154 AN XY: 74302

African (AFR) AF: 0.703 AC: 29156 AN: 41470

American (AMR) AF: 0.399 AC: 6094 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1198 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1102 AN: 5166

South Asian (SAS) AF: 0.328 AC: 1578 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10560

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16099 AN: 67978

Other (OTH) AF: 0.351 AC: 741 AN: 2112

Alfa AF: 0.141 Hom.: 231

Bravo AF: 0.413

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs6050337; hg19: chr20-25097926;