rs10413384

Positions:

• chr19-9073930-G-A
• chr19-9073930-G-C

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 0.223 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

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 (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.229

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10413384; hg19: chr19-9184606;