chr20-46884796-A-G

Variant names:

• chr20-46884796-A-G
• rs1984076

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 0.565 in 152,112 control chromosomes in the GnomAD database, including 24,343 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 0.57 (24343 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.565 AC: 85923 AN: 151994 Hom.: 24325 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.565 AC: 85993 AN: 152112 Hom.: 24343 Cov.: 33 AF XY: 0.567 AC XY: 42167 AN XY: 74348

African (AFR) AF: 0.573 AC: 23802 AN: 41504

American (AMR) AF: 0.563 AC: 8597 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1809 AN: 3472

East Asian (EAS) AF: 0.632 AC: 3274 AN: 5180

South Asian (SAS) AF: 0.507 AC: 2441 AN: 4818

European-Finnish (FIN) AF: 0.589 AC: 6219 AN: 10566

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38124 AN: 67974

Other (OTH) AF: 0.541 AC: 1142 AN: 2112

Alfa AF: 0.568 Hom.: 3360

Bravo AF: 0.566

Asia WGS AF: 0.562 AC: 1951 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.28
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs1984076; hg19: chr20-45513435;