rs713279

Positions:

• chr11-133693414-C-A

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 0.217 in 152,006 control chromosomes in the GnomAD database, including 4,230 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 0.22 (4230 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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: 0.217 AC: 32887 AN: 151888 Hom.: 4213 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.217 AC: 32926 AN: 152006 Hom.: 4230 Cov.: 31 AF XY: 0.225 AC XY: 16735 AN XY: 74306

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.219

Alfa AF: 0.208 Hom.: 8383

Bravo AF: 0.230

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs713279; hg19: chr11-133563309;