rs11597362

Positions:

• chr10-119991375-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 0.0807 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;