rs3809043

Positions:

• chr11-117878400-G-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 0.0472 in 152,226 control chromosomes in the GnomAD database, including 193 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 0.047 (193 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550

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 (EAS) allele frequency at 95% confidence interval = 0.106 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: 0.0472 AC: 7183 AN: 152108 Hom.: 193 Cov.: 33

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.00896

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0472 AC: 7179 AN: 152226 Hom.: 193 Cov.: 33 AF XY: 0.0465 AC XY: 3462 AN XY: 74420

Gnomad4 AFR AF: 0.0599

Gnomad4 AMR AF: 0.0383

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.00896

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0600

Alfa AF: 0.0407 Hom.: 16

Bravo AF: 0.0511

Asia WGS AF: 0.0740 AC: 257 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	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809043; hg19: chr11-117749115;