rs11083752

Positions:

• chr19-44951106-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 0.522 in 151,870 control chromosomes in the GnomAD database, including 21,328 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 0.52 (21317 hom., cov: 30)
  • Exomes 𝑓: 0.39 (11 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44951106G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267114	ENST00000591646.1	n.114-80C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79187 AN: 151646 Hom.: 21282 Cov.: 30

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.394 AC: 41 AN: 104 Hom.: 11 AF XY: 0.378 AC XY: 31 AN XY: 82

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 SAS exome AF: 0.900

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.289

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.522 AC: 79270 AN: 151766 Hom.: 21317 Cov.: 30 AF XY: 0.525 AC XY: 38890 AN XY: 74132

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.502

Alfa AF: 0.520 Hom.: 3067

Bravo AF: 0.534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11083752; hg19: chr19-45454363;