chr20-7279189-C-A

Variant names:

• chr20-7279189-C-A
• rs4239770

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 0.492 in 151,910 control chromosomes in the GnomAD database, including 19,052 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 0.49 (19052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 0 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 (AMR) allele frequency at 95% confidence interval = 0.602 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: 0.492 AC: 74709 AN: 151792 Hom.: 19016 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.492 AC: 74791 AN: 151910 Hom.: 19052 Cov.: 31 AF XY: 0.495 AC XY: 36720 AN XY: 74222

African (AFR) AF: 0.376 AC: 15595 AN: 41438

American (AMR) AF: 0.612 AC: 9334 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1969 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2208 AN: 5134

South Asian (SAS) AF: 0.524 AC: 2525 AN: 4820

European-Finnish (FIN) AF: 0.466 AC: 4918 AN: 10546

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36489 AN: 67938

Other (OTH) AF: 0.533 AC: 1124 AN: 2110

Alfa AF: 0.503 Hom.: 2547

Bravo AF: 0.497

Asia WGS AF: 0.508 AC: 1760 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.62
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs4239770; hg19: chr20-7259836;