rs6090547

Variant names:

• chr20-46749522-T-C
• rs6090547

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 0.57 in 152,046 control chromosomes in the GnomAD database, including 25,743 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 0.57 (25743 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86601 AN: 151928 Hom.: 25697 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.570 AC: 86705 AN: 152046 Hom.: 25743 Cov.: 33 AF XY: 0.577 AC XY: 42866 AN XY: 74326

African (AFR) AF: 0.688 AC: 28524 AN: 41442

American (AMR) AF: 0.548 AC: 8377 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3468

East Asian (EAS) AF: 0.930 AC: 4800 AN: 5162

South Asian (SAS) AF: 0.599 AC: 2888 AN: 4818

European-Finnish (FIN) AF: 0.559 AC: 5899 AN: 10560

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33226 AN: 67992

Other (OTH) AF: 0.547 AC: 1157 AN: 2114

Alfa AF: 0.513 Hom.: 27070

Bravo AF: 0.572

Asia WGS AF: 0.761 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.094
DANN	Benign	0.41
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6090547; hg19: chr20-45378161;