rs11258317

Positions:

• chr10-6365775-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 0.32 in 152,044 control chromosomes in the GnomAD database, including 8,354 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 0.32 (8354 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

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 (NFE) allele frequency at 95% confidence interval = 0.379 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: 0.320 AC: 48632 AN: 151926 Hom.: 8352 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.320 AC: 48662 AN: 152044 Hom.: 8354 Cov.: 32 AF XY: 0.320 AC XY: 23766 AN XY: 74318

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.0293

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.326

Alfa AF: 0.357 Hom.: 9551

Bravo AF: 0.304

Asia WGS AF: 0.148 AC: 518 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	0.70
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11258317; hg19: chr10-6407737;