11-18050016-T-G

Position:

• chr11-18050016-T-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 0.47 in 151,804 control chromosomes in the GnomAD database, including 18,207 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 0.47 (18207 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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: 0.470 AC: 71286 AN: 151684 Hom.: 18159 Cov.: 30

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.470 AC: 71390 AN: 151804 Hom.: 18207 Cov.: 30 AF XY: 0.461 AC XY: 34221 AN XY: 74156

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.457

Alfa AF: 0.386 Hom.: 3296

Bravo AF: 0.479

Asia WGS AF: 0.321 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7110238; hg19: chr11-18071563;