20-48426526-C-T

Variant names:

• chr20-48426526-C-T
• rs999151

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.321

Alfa AF: 0.309 Hom.: 3475

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999151; hg19: chr20-47055269;