rs11597390

chr10-100101678-G-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 0.291 in 151,956 control chromosomes in the GnomAD database, including 6,987 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 0.29 (6987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 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: 0.291 AC: 44204 AN: 151838 Hom.: 6977 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.0678

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.291 AC: 44239 AN: 151956 Hom.: 6987 Cov.: 32 AF XY: 0.286 AC XY: 21224 AN XY: 74248

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.0674

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.322

Alfa AF: 0.345 Hom.: 16166

Bravo AF: 0.296

Asia WGS AF: 0.128 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.029
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: rs11597390; hg19: chr10-101861435;