rs730270

chr20-7793055-T-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 0.114 in 152,200 control chromosomes in the GnomAD database, including 1,166 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 0.11 (1166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17273 AN: 152082 Hom.: 1159 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.114 AC: 17300 AN: 152200 Hom.: 1166 Cov.: 32 AF XY: 0.115 AC XY: 8574 AN XY: 74422

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.0483

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0967 Hom.: 194

Bravo AF: 0.120

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730270; hg19: chr20-7773702;