rs11665841

Positions:

• chr19-48758444-C-T

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 0.0717 in 409,302 control chromosomes in the GnomAD database, including 2,801 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 0.072 (640 hom., cov: 31)
  • Exomes 𝑓: 0.071 (2161 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48758444C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10855 AN: 150144 Hom.: 637 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0752

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0335

Gnomad OTH AF: 0.0611

GnomAD4 exome AF: 0.0713 AC: 18462 AN: 259054 Hom.: 2161 AF XY: 0.0698 AC XY: 9254 AN XY: 132650

Gnomad4 AFR exome AF: 0.120

Gnomad4 AMR exome AF: 0.0931

Gnomad4 ASJ exome AF: 0.0203

Gnomad4 EAS exome AF: 0.408

Gnomad4 SAS exome AF: 0.108

Gnomad4 FIN exome AF: 0.0231

Gnomad4 NFE exome AF: 0.0326

Gnomad4 OTH exome AF: 0.0586

GnomAD4 genome AF: 0.0724 AC: 10876 AN: 150248 Hom.: 640 Cov.: 31 AF XY: 0.0746 AC XY: 5469 AN XY: 73356

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0898

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.0614

Alfa AF: 0.0572 Hom.: 40

Bravo AF: 0.0796

Asia WGS AF: 0.205 AC: 710 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11665841; hg19: chr19-49261701;