chr20-11998547-C-T

Variant names:

• chr20-11998547-C-T
• rs10485751

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 0.0513 in 152,062 control chromosomes in the GnomAD database, including 440 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 0.051 (440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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: 0.0512 AC: 7780 AN: 151944 Hom.: 437 Cov.: 32

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.00377

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0513 AC: 7795 AN: 152062 Hom.: 440 Cov.: 32 AF XY: 0.0547 AC XY: 4069 AN XY: 74334

African (AFR) AF: 0.0777 AC: 3220 AN: 41450

American (AMR) AF: 0.0920 AC: 1406 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1113 AN: 5146

South Asian (SAS) AF: 0.144 AC: 695 AN: 4812

European-Finnish (FIN) AF: 0.00377 AC: 40 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0163 AC: 1106 AN: 67984

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0304 Hom.: 798

Bravo AF: 0.0567

Asia WGS AF: 0.159 AC: 552 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	3.1
DANN	Benign	0.57
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10485751; hg19: chr20-11979195;