rs11256463

Positions:

• chr10-10049303-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 0.396 in 151,942 control chromosomes in the GnomAD database, including 12,163 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 0.40 (12163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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: 0.396 AC: 60069 AN: 151822 Hom.: 12147 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.396 AC: 60123 AN: 151942 Hom.: 12163 Cov.: 32 AF XY: 0.401 AC XY: 29775 AN XY: 74268

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.391

Alfa AF: 0.390 Hom.: 10921

Bravo AF: 0.378

Asia WGS AF: 0.375 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11256463; hg19: chr10-10091266;