rs794070

Variant names:

• chr19-7649928-A-G
• rs794070

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 0.245 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.276 AC: 11412 AN: 41398

American (AMR) AF: 0.308 AC: 4680 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3466

East Asian (EAS) AF: 0.143 AC: 740 AN: 5172

South Asian (SAS) AF: 0.141 AC: 681 AN: 4814

European-Finnish (FIN) AF: 0.249 AC: 2624 AN: 10530

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15521 AN: 67938

Other (OTH) AF: 0.232 AC: 489 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.30
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs794070; hg19: chr19-7714814;