chr20-60081096-T-C

Variant names:

• chr20-60081096-T-C
• rs6027281

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 0.307 in 151,740 control chromosomes in the GnomAD database, including 8,064 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 0.31 (8064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.307 AC: 46473 AN: 151624 Hom.: 8046 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.307 AC: 46539 AN: 151740 Hom.: 8064 Cov.: 32 AF XY: 0.300 AC XY: 22276 AN XY: 74156

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.00291

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.298

Alfa AF: 0.302 Hom.: 1482

Bravo AF: 0.308

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6027281; hg19: chr20-58656151;