rs11665668

chr19-51666449-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;