rs10412302

chr19-56886142-T-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 0.328 in 152,044 control chromosomes in the GnomAD database, including 8,394 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 0.33 (8394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49867 AN: 151926 Hom.: 8382 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.328 AC: 49921 AN: 152044 Hom.: 8394 Cov.: 32 AF XY: 0.325 AC XY: 24131 AN XY: 74320

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.344

Alfa AF: 0.337 Hom.: 1571

Bravo AF: 0.334

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.5
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10412302; hg19: chr19-57397510;