rs10896449

Positions:

• chr11-69227200-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 0.523 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;