rs11593319

Variant names:

• chr10-46069929-C-A
• rs11593319

Your query was ambiguous. Multiple possible variants found:

• chr10-46069929-C-A
• chr10-46069929-C-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;