rs11030043

Positions:

• chr11-3846120-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 0.0692 in 152,236 control chromosomes in the GnomAD database, including 472 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 0.069 (472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 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: 0.0693 AC: 10543 AN: 152118 Hom.: 473 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0692 AC: 10535 AN: 152236 Hom.: 472 Cov.: 32 AF XY: 0.0665 AC XY: 4953 AN XY: 74428

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0492

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.104 Hom.: 1179

Bravo AF: 0.0701

Asia WGS AF: 0.0210 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11030043; hg19: chr11-3867350; COSMIC: COSV53391733;