rs6048344

chr20-22790726-G-Cchr20-22790726-G-T

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 0.47 in 152,070 control chromosomes in the GnomAD database, including 19,016 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 0.47 (19016 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71491 AN: 151952 Hom.: 19017 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.470 AC: 71491 AN: 152070 Hom.: 19016 Cov.: 33 AF XY: 0.470 AC XY: 34940 AN XY: 74344

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.499

Alfa AF: 0.349 Hom.: 945

Bravo AF: 0.472

Asia WGS AF: 0.571 AC: 1985 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.75
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6048344; hg19: chr20-22771364;