rs11665668

Variant names:

• chr19-51666449-G-A
• rs11665668

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 0.0502 in 152,056 control chromosomes in the GnomAD database, including 293 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 0.050 (293 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0709 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: 0.0502 AC: 7627 AN: 151938 Hom.: 293 Cov.: 31

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0414

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

GnomAD4 genome AF: 0.0502 AC: 7630 AN: 152056 Hom.: 293 Cov.: 31 AF XY: 0.0512 AC XY: 3802 AN XY: 74318

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0324

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0203

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.0410

Alfa AF: 0.0622 Hom.: 319

Bravo AF: 0.0404

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11665668; hg19: chr19-52169702;