11-18046616-C-A

Position:

• chr11-18046616-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 0.4 in 151,902 control chromosomes in the GnomAD database, including 12,396 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 0.40 (12396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.400 AC: 60706 AN: 151784 Hom.: 12386 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.400 AC: 60762 AN: 151902 Hom.: 12396 Cov.: 31 AF XY: 0.394 AC XY: 29249 AN XY: 74226

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.415

Alfa AF: 0.410 Hom.: 17210

Bravo AF: 0.399

Asia WGS AF: 0.301 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7130929; hg19: chr11-18068163;