rs353589

Positions:

• chr11-35099679-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 0.298 in 152,150 control chromosomes in the GnomAD database, including 8,612 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 0.30 (8612 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 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: 0.297 AC: 45188 AN: 152032 Hom.: 8563 Cov.: 33

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.298 AC: 45315 AN: 152150 Hom.: 8612 Cov.: 33 AF XY: 0.300 AC XY: 22295 AN XY: 74400

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.281

Alfa AF: 0.211 Hom.: 3791

Bravo AF: 0.312

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353589; hg19: chr11-35121226;