rs11597362

Variant names:

• chr10-119991375-C-T
• rs11597362

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 0.0807 in 152,226 control chromosomes in the GnomAD database, including 577 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 0.081 (577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.107 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: 0.0808 AC: 12287 AN: 152108 Hom.: 576 Cov.: 32

Gnomad AFR AF: 0.0641

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0657

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.0838

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

GnomAD4 genome AF: 0.0807 AC: 12285 AN: 152226 Hom.: 577 Cov.: 32 AF XY: 0.0806 AC XY: 6000 AN XY: 74416

Gnomad4 AFR AF: 0.0641

Gnomad4 AMR AF: 0.0657

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.0820

Alfa AF: 0.0898 Hom.: 95

Bravo AF: 0.0771

Asia WGS AF: 0.0350 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11597362; hg19: chr10-121750887;