rs10896450

Positions:

• chr11-69240647-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;