20-24790993-C-T

Variant names:

• chr20-24790993-C-T
• rs226679

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 0.508 in 152,056 control chromosomes in the GnomAD database, including 20,802 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 0.51 (20802 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.508 AC: 77141 AN: 151938 Hom.: 20798 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.508 AC: 77171 AN: 152056 Hom.: 20802 Cov.: 33 AF XY: 0.512 AC XY: 38027 AN XY: 74324

African (AFR) AF: 0.351 AC: 14583 AN: 41488

American (AMR) AF: 0.527 AC: 8058 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1652 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4941 AN: 5174

South Asian (SAS) AF: 0.585 AC: 2815 AN: 4808

European-Finnish (FIN) AF: 0.550 AC: 5813 AN: 10572

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37372 AN: 67952

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.351 Hom.: 996

Bravo AF: 0.502

Asia WGS AF: 0.731 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs226679; hg19: chr20-24771629;