chr19-9073930-G-A

Variant names:

• chr19-9073930-G-A
• rs10413384

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 0.223 in 151,836 control chromosomes in the GnomAD database, including 3,832 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 0.22 (3832 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.314 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: 0.223 AC: 33827 AN: 151716 Hom.: 3827 Cov.: 30

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.223 AC: 33847 AN: 151836 Hom.: 3832 Cov.: 30 AF XY: 0.223 AC XY: 16561 AN XY: 74176

African (AFR) AF: 0.216 AC: 8944 AN: 41414

American (AMR) AF: 0.198 AC: 3013 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3466

East Asian (EAS) AF: 0.162 AC: 833 AN: 5144

South Asian (SAS) AF: 0.327 AC: 1571 AN: 4798

European-Finnish (FIN) AF: 0.201 AC: 2116 AN: 10550

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15905 AN: 67932

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.218 Hom.: 681

Bravo AF: 0.220

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.56
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10413384; hg19: chr19-9184606;