20-48249703-T-C

Variant names:

• chr20-48249703-T-C
• rs226844

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 0.9 in 152,132 control chromosomes in the GnomAD database, including 61,723 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 0.90 (61723 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 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 = 0.955 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: 0.900 AC: 136757 AN: 152014 Hom.: 61674 Cov.: 30

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.900 AC: 136864 AN: 152132 Hom.: 61723 Cov.: 30 AF XY: 0.901 AC XY: 66974 AN XY: 74368

African (AFR) AF: 0.839 AC: 34817 AN: 41480

American (AMR) AF: 0.936 AC: 14322 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3104 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5058 AN: 5172

South Asian (SAS) AF: 0.812 AC: 3903 AN: 4804

European-Finnish (FIN) AF: 0.951 AC: 10085 AN: 10608

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62622 AN: 67986

Other (OTH) AF: 0.895 AC: 1884 AN: 2104

Alfa AF: 0.906 Hom.: 12050

Bravo AF: 0.897

Asia WGS AF: 0.892 AC: 3102 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	0.076
DANN	Benign	0.50
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs226844; hg19: chr20-46878446;