rs10511813

chr9-27664164-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 0.158 in 152,072 control chromosomes in the GnomAD database, including 2,413 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 0.16 (2413 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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: 0.158 AC: 24026 AN: 151954 Hom.: 2410 Cov.: 30

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.158 AC: 24031 AN: 152072 Hom.: 2413 Cov.: 30 AF XY: 0.156 AC XY: 11576 AN XY: 74328

Gnomad4 AFR AF: 0.0542

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.202

Alfa AF: 0.211 Hom.: 4941

Bravo AF: 0.157

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.29
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511813; hg19: chr9-27664162;