rs10896449

Variant names:

• chr11-69227200-A-G
• rs10896449

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 0.523 in 152,026 control chromosomes in the GnomAD database, including 22,269 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 0.52 (22269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

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 (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.523 AC: 79447 AN: 151908 Hom.: 22233 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.523 AC: 79536 AN: 152026 Hom.: 22269 Cov.: 32 AF XY: 0.515 AC XY: 38251 AN XY: 74308

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.0683

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.536

Alfa AF: 0.504 Hom.: 31807

Bravo AF: 0.527

Asia WGS AF: 0.298 AC: 1038 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	3.7
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10896449; hg19: chr11-68994667;