rs10894727

Positions:

• chr11-133694740-T-C

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 0.555 in 152,052 control chromosomes in the GnomAD database, including 24,616 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 0.56 (24616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

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 (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.555 AC: 84364 AN: 151934 Hom.: 24601 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.555 AC: 84410 AN: 152052 Hom.: 24616 Cov.: 32 AF XY: 0.570 AC XY: 42386 AN XY: 74312

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.537

Alfa AF: 0.552 Hom.: 22715

Bravo AF: 0.545

Asia WGS AF: 0.852 AC: 2962 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	6.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10894727; hg19: chr11-133564635;