rs10413807

Positions:

• chr19-7659742-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 0.205 in 151,914 control chromosomes in the GnomAD database, including 3,174 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 0.21 (3174 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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 = 0.236 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: 0.205 AC: 31121 AN: 151796 Hom.: 3167 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.205 AC: 31166 AN: 151914 Hom.: 3174 Cov.: 31 AF XY: 0.204 AC XY: 15140 AN XY: 74242

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.199

Alfa AF: 0.209 Hom.: 405

Bravo AF: 0.197

Asia WGS AF: 0.226 AC: 787 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	3.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10413807; hg19: chr19-7724628;