20-23598646-T-C

Variant names:

• chr20-23598646-T-C
• rs2093145

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 0.494 in 151,928 control chromosomes in the GnomAD database, including 21,503 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 0.49 (21503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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: 0.494 AC: 75070 AN: 151814 Hom.: 21498 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.494 AC: 75085 AN: 151928 Hom.: 21503 Cov.: 32 AF XY: 0.501 AC XY: 37232 AN XY: 74288

African (AFR) AF: 0.181 AC: 7496 AN: 41482

American (AMR) AF: 0.626 AC: 9559 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2121 AN: 3472

East Asian (EAS) AF: 0.692 AC: 3576 AN: 5170

South Asian (SAS) AF: 0.493 AC: 2375 AN: 4820

European-Finnish (FIN) AF: 0.663 AC: 6971 AN: 10508

Middle Eastern (MID) AF: 0.638 AC: 185 AN: 290

European-Non Finnish (NFE) AF: 0.605 AC: 41068 AN: 67906

Other (OTH) AF: 0.525 AC: 1104 AN: 2104

Alfa AF: 0.532 Hom.: 4035

Bravo AF: 0.481

Asia WGS AF: 0.554 AC: 1925 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs2093145; hg19: chr20-23579283;