20-53515390-T-C

Variant names:

• chr20-53515390-T-C
• rs915049

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 0.936 in 152,264 control chromosomes in the GnomAD database, including 66,766 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 0.94 (66766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.971 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: 0.936 AC: 142385 AN: 152146 Hom.: 66709 Cov.: 32

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.936 AC: 142496 AN: 152264 Hom.: 66766 Cov.: 32 AF XY: 0.934 AC XY: 69550 AN XY: 74436

African (AFR) AF: 0.979 AC: 40677 AN: 41544

American (AMR) AF: 0.943 AC: 14412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3057 AN: 3472

East Asian (EAS) AF: 0.833 AC: 4317 AN: 5184

South Asian (SAS) AF: 0.910 AC: 4395 AN: 4832

European-Finnish (FIN) AF: 0.880 AC: 9334 AN: 10604

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63172 AN: 68024

Other (OTH) AF: 0.930 AC: 1968 AN: 2116

Alfa AF: 0.927 Hom.: 89486

Bravo AF: 0.942

Asia WGS AF: 0.874 AC: 3041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.55
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs915049; hg19: chr20-52131929;