chr20-22760259-T-C

Variant names:

• chr20-22760259-T-C
• rs2424460

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 0.635 in 152,028 control chromosomes in the GnomAD database, including 31,048 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 0.64 (31048 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.635 AC: 96522 AN: 151910 Hom.: 31028 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.635 AC: 96584 AN: 152028 Hom.: 31048 Cov.: 31 AF XY: 0.636 AC XY: 47289 AN XY: 74306

African (AFR) AF: 0.660 AC: 27352 AN: 41450

American (AMR) AF: 0.690 AC: 10550 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2396 AN: 3466

East Asian (EAS) AF: 0.947 AC: 4880 AN: 5152

South Asian (SAS) AF: 0.678 AC: 3263 AN: 4810

European-Finnish (FIN) AF: 0.559 AC: 5915 AN: 10578

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40163 AN: 67972

Other (OTH) AF: 0.637 AC: 1342 AN: 2106

Alfa AF: 0.613 Hom.: 54435

Bravo AF: 0.647

Asia WGS AF: 0.779 AC: 2710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.62
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs2424460; hg19: chr20-22740897;