chr20-57483299-A-T

Variant names:

• chr20-57483299-A-T
• rs59972978

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 0.177 in 152,130 control chromosomes in the GnomAD database, including 3,194 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 0.18 (3194 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 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: 0.177 AC: 26927 AN: 152012 Hom.: 3180 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.177 AC: 26949 AN: 152130 Hom.: 3194 Cov.: 32 AF XY: 0.185 AC XY: 13755 AN XY: 74376

African (AFR) AF: 0.0370 AC: 1538 AN: 41530

American (AMR) AF: 0.323 AC: 4930 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1732 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1087 AN: 4820

European-Finnish (FIN) AF: 0.288 AC: 3046 AN: 10572

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13413 AN: 67980

Other (OTH) AF: 0.172 AC: 362 AN: 2104

Alfa AF: 0.123 Hom.: 276

Bravo AF: 0.174

Asia WGS AF: 0.276 AC: 959 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	4.6
DANN	Benign	0.69
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs59972978; hg19: chr20-56058355;