rs2018368

Positions:

• chr11-10718819-C-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 0.594 in 151,974 control chromosomes in the GnomAD database, including 27,919 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 0.59 (27919 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 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: 0.594 AC: 90160 AN: 151854 Hom.: 27867 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.594 AC: 90271 AN: 151974 Hom.: 27919 Cov.: 31 AF XY: 0.594 AC XY: 44081 AN XY: 74260

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.599

Alfa AF: 0.538 Hom.: 2814

Bravo AF: 0.623

Asia WGS AF: 0.673 AC: 2336 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	0.62
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2018368; hg19: chr11-10740366;