rs794070

chr19-7649928-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 0.245 in 151,832 control chromosomes in the GnomAD database, including 4,753 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 0.24 (4753 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 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: 0.245 AC: 37146 AN: 151714 Hom.: 4735 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.245 AC: 37195 AN: 151832 Hom.: 4753 Cov.: 31 AF XY: 0.244 AC XY: 18121 AN XY: 74206

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.232

Alfa AF: 0.236 Hom.: 884

Bravo AF: 0.254

Asia WGS AF: 0.166 AC: 576 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs794070; hg19: chr19-7714814;