20-45352086-T-C

Variant names:

• chr20-45352086-T-C
• rs1008953

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 0.791 in 152,168 control chromosomes in the GnomAD database, including 47,843 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 0.79 (47843 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 47 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 (AFR) allele frequency at 95% confidence interval = 0.845 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: 0.791 AC: 120218 AN: 152050 Hom.: 47787 Cov.: 33

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.791 AC: 120332 AN: 152168 Hom.: 47843 Cov.: 33 AF XY: 0.789 AC XY: 58689 AN XY: 74388

African (AFR) AF: 0.853 AC: 35401 AN: 41526

American (AMR) AF: 0.784 AC: 11985 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2908 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2823 AN: 5178

South Asian (SAS) AF: 0.794 AC: 3827 AN: 4818

European-Finnish (FIN) AF: 0.757 AC: 8009 AN: 10584

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52788 AN: 67996

Other (OTH) AF: 0.792 AC: 1667 AN: 2104

Alfa AF: 0.780 Hom.: 191872

Bravo AF: 0.791

Asia WGS AF: 0.726 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1008953; hg19: chr20-43980726;