rs11662297

Variant names:

• chr18-6668051-A-G
• rs11662297

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 0.459 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.480 AC: 19863 AN: 41420

American (AMR) AF: 0.418 AC: 6379 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3470

East Asian (EAS) AF: 0.128 AC: 663 AN: 5170

South Asian (SAS) AF: 0.411 AC: 1977 AN: 4810

European-Finnish (FIN) AF: 0.464 AC: 4886 AN: 10528

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32663 AN: 67958

Other (OTH) AF: 0.462 AC: 977 AN: 2114

Alfa AF: 0.460 Hom.: 14432

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs11662297; hg19: chr18-6668050;