rs11030043

Variant names:

• chr11-3846120-A-G
• rs11030043

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0176 AC: 730 AN: 41544

American (AMR) AF: 0.0765 AC: 1170 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0492 AC: 237 AN: 4820

European-Finnish (FIN) AF: 0.0608 AC: 645 AN: 10600

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7081 AN: 67996

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.100 Hom.: 1419

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
PhyloP100		0.34

Splicing

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

Other links and lift over

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