rs6056327

Variant names:

• chr20-9007765-C-T
• rs6056327

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 0.317 in 151,970 control chromosomes in the GnomAD database, including 9,544 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 (9544 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.317 AC: 48088 AN: 151852 Hom.: 9530 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.317 AC: 48153 AN: 151970 Hom.: 9544 Cov.: 32 AF XY: 0.321 AC XY: 23829 AN XY: 74260

African (AFR) AF: 0.508 AC: 21062 AN: 41436

American (AMR) AF: 0.255 AC: 3887 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3472

East Asian (EAS) AF: 0.700 AC: 3602 AN: 5148

South Asian (SAS) AF: 0.443 AC: 2132 AN: 4812

European-Finnish (FIN) AF: 0.243 AC: 2561 AN: 10556

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13539 AN: 67968

Other (OTH) AF: 0.263 AC: 555 AN: 2110

Alfa AF: 0.236 Hom.: 21592

Bravo AF: 0.322

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.50
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6056327; hg19: chr20-8988412;