rs11596854

chr10-46330334-A-G

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 0.364 in 515,298 control chromosomes in the GnomAD database, including 35,878 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 0.34 (9596 hom., cov: 33)
  • Exomes 𝑓: 0.38 (26282 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.438 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: 0.336 AC: 50891 AN: 151630 Hom.: 9600 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.345

GnomAD4 exome AF: 0.375 AC: 136426 AN: 363550 Hom.: 26282 AF XY: 0.372 AC XY: 69827 AN XY: 187936

Gnomad4 AFR exome AF: 0.129

Gnomad4 AMR exome AF: 0.470

Gnomad4 ASJ exome AF: 0.384

Gnomad4 EAS exome AF: 0.225

Gnomad4 SAS exome AF: 0.281

Gnomad4 FIN exome AF: 0.455

Gnomad4 NFE exome AF: 0.403

Gnomad4 OTH exome AF: 0.362

GnomAD4 genome AF: 0.335 AC: 50891 AN: 151748 Hom.: 9596 Cov.: 33 AF XY: 0.338 AC XY: 25080 AN XY: 74156

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.340

Alfa AF: 0.403 Hom.: 23583

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.3
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11596854; hg19: chr10-47701570;