20-48426526-C-T

Variant names:

• chr20-48426526-C-T
• rs999151

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 0.324 in 151,882 control chromosomes in the GnomAD database, including 8,271 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 0.32 (8271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 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: 0.323 AC: 49095 AN: 151764 Hom.: 8256 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.324 AC: 49136 AN: 151882 Hom.: 8271 Cov.: 32 AF XY: 0.325 AC XY: 24125 AN XY: 74208

African (AFR) AF: 0.322 AC: 13345 AN: 41392

American (AMR) AF: 0.448 AC: 6845 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2128 AN: 5162

South Asian (SAS) AF: 0.297 AC: 1425 AN: 4806

European-Finnish (FIN) AF: 0.297 AC: 3133 AN: 10544

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20340 AN: 67922

Other (OTH) AF: 0.321 AC: 680 AN: 2116

Alfa AF: 0.308 Hom.: 3807

Bravo AF: 0.338

Asia WGS AF: 0.326 AC: 1132 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	1.6
DANN	Benign	0.60
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs999151; hg19: chr20-47055269;