rs10896450

Variant names:

• chr11-69240647-A-G
• rs10896450

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 0.537 in 152,100 control chromosomes in the GnomAD database, including 23,701 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 0.54 (23701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 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: 0.537 AC: 81560 AN: 151982 Hom.: 23657 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.537 AC: 81657 AN: 152100 Hom.: 23701 Cov.: 32 AF XY: 0.529 AC XY: 39306 AN XY: 74344

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.0635

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.550

Alfa AF: 0.503 Hom.: 10546

Bravo AF: 0.541

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10896450; hg19: chr11-69008114;