rs10896468

Variant names:

• chr11-56509110-G-T
• rs10896468

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 0.173 in 152,122 control chromosomes in the GnomAD database, including 2,679 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 0.17 (2679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 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: 0.173 AC: 26310 AN: 152004 Hom.: 2680 Cov.: 32

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.173 AC: 26304 AN: 152122 Hom.: 2679 Cov.: 32 AF XY: 0.171 AC XY: 12746 AN XY: 74356

Gnomad4 AFR AF: 0.0615

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.170

Alfa AF: 0.195 Hom.: 453

Bravo AF: 0.163

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10896468; hg19: chr11-56276586;