rs11602906

chr11-73973249-G-Achr11-73973249-G-T

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 0.0565 in 152,268 control chromosomes in the GnomAD database, including 381 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 0.056 (381 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8600 AN: 152150 Hom.: 380 Cov.: 33

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0565 AC: 8598 AN: 152268 Hom.: 381 Cov.: 33 AF XY: 0.0597 AC XY: 4447 AN XY: 74440

Gnomad4 AFR AF: 0.0141

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.0550

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0656 Hom.: 463

Bravo AF: 0.0445

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.51
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11602906; hg19: chr11-73684294;