20-54846436-C-T

Variant names:

• chr20-54846436-C-T
• rs1512060

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0174 in 152,142 control chromosomes in the GnomAD database, including 29 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 0.017 (29 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0174 (2648/152142) while in subpopulation NFE AF = 0.0283 (1925/68000). AF 95% confidence interval is 0.0273. There are 29 homozygotes in GnomAd4. There are 1250 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 29 gene

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: 0.0174 AC: 2649 AN: 152024 Hom.: 29 Cov.: 32

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00644

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0174 AC: 2648 AN: 152142 Hom.: 29 Cov.: 32 AF XY: 0.0168 AC XY: 1250 AN XY: 74368

African (AFR) AF: 0.00518 AC: 215 AN: 41514

American (AMR) AF: 0.0168 AC: 256 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.00864 AC: 30 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00644 AC: 31 AN: 4810

European-Finnish (FIN) AF: 0.0139 AC: 148 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0283 AC: 1925 AN: 68000

Other (OTH) AF: 0.0161 AC: 34 AN: 2110

Alfa AF: 0.0257 Hom.: 87

Bravo AF: 0.0168

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.74
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1512060; hg19: chr20-53462975;