20-7278822-A-G

Position:

• chr20-7278822-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.492 in 151,778 control chromosomes in the GnomAD database, including 19,032 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 (19032 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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/exons	MANE	Protein	UniProt
		n.7278822A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74643 AN: 151658 Hom.: 18996 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.468

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: 74725 AN: 151778 Hom.: 19032 Cov.: 31 AF XY: 0.495 AC XY: 36687 AN XY: 74148

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.533

Alfa AF: 0.520 Hom.: 3508

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	-0.92
CADD	Benign	2.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2326909; hg19: chr20-7259469;