rs6048205

chr20-22578963-A-G

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 0.09 in 151,904 control chromosomes in the GnomAD database, including 859 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 0.090 (859 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.0898 AC: 13635 AN: 151786 Hom.: 850 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0408

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0900 AC: 13667 AN: 151904 Hom.: 859 Cov.: 31 AF XY: 0.0880 AC XY: 6531 AN XY: 74234

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0511

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.0325

Gnomad4 FIN AF: 0.0408

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.0581 Hom.: 403

Bravo AF: 0.0959

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.9
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6048205; hg19: chr20-22559601;