20-57108940-T-C

Variant names:

• chr20-57108940-T-C
• rs11699237

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 0.1 in 152,180 control chromosomes in the GnomAD database, including 1,078 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 0.10 (1078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.62
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.100 AC: 15218 AN: 152062 Hom.: 1075 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.0710

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.100 AC: 15244 AN: 152180 Hom.: 1078 Cov.: 32 AF XY: 0.0984 AC XY: 7321 AN XY: 74420

African (AFR) AF: 0.200 AC: 8302 AN: 41492

American (AMR) AF: 0.0661 AC: 1011 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0505 AC: 175 AN: 3468

East Asian (EAS) AF: 0.0705 AC: 364 AN: 5160

South Asian (SAS) AF: 0.0481 AC: 232 AN: 4822

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0654 AC: 4450 AN: 68008

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0816 Hom.: 1188

Bravo AF: 0.107

Asia WGS AF: 0.0720 AC: 252 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	0.29
DANN	Benign	0.33
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs11699237; hg19: chr20-55683996;