rs11593319

Positions:

• chr10-46069929-C-A

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 0.0491 in 152,220 control chromosomes in the GnomAD database, including 261 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 0.049 (261 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0674 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: 0.0491 AC: 7472 AN: 152102 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0525

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

GnomAD4 genome AF: 0.0491 AC: 7477 AN: 152220 Hom.: 261 Cov.: 32 AF XY: 0.0495 AC XY: 3684 AN XY: 74428

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.0690

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0613 Hom.: 129

Bravo AF: 0.0436

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.3
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11593319; hg19: chr10-51525893;