rs11662297

chr18-6668051-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 0.459 in 151,932 control chromosomes in the GnomAD database, including 16,360 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 0.46 (16360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 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: 0.459 AC: 69636 AN: 151812 Hom.: 16331 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.459 AC: 69709 AN: 151932 Hom.: 16360 Cov.: 32 AF XY: 0.455 AC XY: 33821 AN XY: 74274

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.462

Alfa AF: 0.464 Hom.: 6450

Bravo AF: 0.456

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.55
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11662297; hg19: chr18-6668050;