rs10413807

Variant names:

• chr19-7659742-G-C
• rs10413807

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 0.205 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
• Publications: 2 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 = 0.236 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: 0.205 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

African (AFR) AF: 0.224 AC: 9278 AN: 41416

American (AMR) AF: 0.144 AC: 2200 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3470

East Asian (EAS) AF: 0.184 AC: 951 AN: 5168

South Asian (SAS) AF: 0.247 AC: 1191 AN: 4816

European-Finnish (FIN) AF: 0.230 AC: 2417 AN: 10530

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13903 AN: 67926

Other (OTH) AF: 0.199 AC: 420 AN: 2112

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10413807; hg19: chr19-7724628;