chr20-59053184-C-T

Variant names:

• chr20-59053184-C-T
• rs6070706

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 0.115 in 152,124 control chromosomes in the GnomAD database, including 1,232 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 0.11 (1232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 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: 0.115 AC: 17432 AN: 152006 Hom.: 1233 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.115 AC: 17425 AN: 152124 Hom.: 1232 Cov.: 32 AF XY: 0.120 AC XY: 8915 AN XY: 74360

African (AFR) AF: 0.0610 AC: 2532 AN: 41526

American (AMR) AF: 0.0892 AC: 1363 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3470

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5180

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4826

European-Finnish (FIN) AF: 0.263 AC: 2778 AN: 10550

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9430 AN: 67978

Other (OTH) AF: 0.0991 AC: 209 AN: 2108

Alfa AF: 0.125 Hom.: 2105

Bravo AF: 0.0992

Asia WGS AF: 0.0490 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6070706; hg19: chr20-57628239;