rs6056327

Variant names:

• chr20-9007765-C-T
• rs6056327

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 0.317 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.317 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

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.263

Alfa AF: 0.218 Hom.: 8720

Bravo AF: 0.322

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6056327; hg19: chr20-8988412;