20-46172387-A-G

Variant names:

• chr20-46172387-A-G
• rs1321000

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 0.738 in 152,066 control chromosomes in the GnomAD database, including 42,020 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 0.74 (42020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 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: 0.738 AC: 112157 AN: 151948 Hom.: 41963 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.738 AC: 112265 AN: 152066 Hom.: 42020 Cov.: 31 AF XY: 0.732 AC XY: 54428 AN XY: 74320

African (AFR) AF: 0.874 AC: 36298 AN: 41512

American (AMR) AF: 0.705 AC: 10772 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2680 AN: 3470

East Asian (EAS) AF: 0.568 AC: 2919 AN: 5138

South Asian (SAS) AF: 0.631 AC: 3035 AN: 4812

European-Finnish (FIN) AF: 0.649 AC: 6853 AN: 10560

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47290 AN: 67978

Other (OTH) AF: 0.740 AC: 1560 AN: 2108

Alfa AF: 0.711 Hom.: 55843

Bravo AF: 0.749

Asia WGS AF: 0.669 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.8
DANN	Benign	0.84
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1321000; hg19: chr20-44801026;