rs6048205

Variant names:

• chr20-22578963-A-G
• rs6048205

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 0.09 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
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.177 AC: 7306 AN: 41384

American (AMR) AF: 0.0511 AC: 780 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3472

East Asian (EAS) AF: 0.159 AC: 818 AN: 5130

South Asian (SAS) AF: 0.0325 AC: 156 AN: 4798

European-Finnish (FIN) AF: 0.0408 AC: 431 AN: 10562

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0515 AC: 3502 AN: 67988

Other (OTH) AF: 0.0871 AC: 184 AN: 2112

Alfa AF: 0.0618 Hom.: 1037

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
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs6048205; hg19: chr20-22559601;