chr20-59012716-C-T

Variant names:

• chr20-59012716-C-T
• rs4812048

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 0.149 in 152,216 control chromosomes in the GnomAD database, including 1,948 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 0.15 (1948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 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: 0.149 AC: 22650 AN: 152098 Hom.: 1947 Cov.: 33

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.149 AC: 22663 AN: 152216 Hom.: 1948 Cov.: 33 AF XY: 0.155 AC XY: 11525 AN XY: 74404

African (AFR) AF: 0.0806 AC: 3350 AN: 41548

American (AMR) AF: 0.136 AC: 2079 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3470

East Asian (EAS) AF: 0.0838 AC: 434 AN: 5182

South Asian (SAS) AF: 0.179 AC: 865 AN: 4828

European-Finnish (FIN) AF: 0.278 AC: 2938 AN: 10568

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12030 AN: 68008

Other (OTH) AF: 0.135 AC: 285 AN: 2116

Alfa AF: 0.160 Hom.: 3998

Bravo AF: 0.135

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.72
DANN	Benign	0.60
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs4812048; hg19: chr20-57587771;