20-7466544-A-G

Variant names:

• chr20-7466544-A-G
• rs2326931

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 0.609 in 151,842 control chromosomes in the GnomAD database, including 28,367 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 0.61 (28367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92347 AN: 151724 Hom.: 28347 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.609 AC: 92410 AN: 151842 Hom.: 28367 Cov.: 32 AF XY: 0.605 AC XY: 44888 AN XY: 74216

African (AFR) AF: 0.566 AC: 23440 AN: 41432

American (AMR) AF: 0.579 AC: 8833 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2212 AN: 3466

East Asian (EAS) AF: 0.745 AC: 3849 AN: 5164

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4820

European-Finnish (FIN) AF: 0.592 AC: 6234 AN: 10538

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43328 AN: 67860

Other (OTH) AF: 0.610 AC: 1284 AN: 2106

Alfa AF: 0.620 Hom.: 3858

Bravo AF: 0.607

Asia WGS AF: 0.633 AC: 2197 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.52
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2326931; hg19: chr20-7447191;