rs11083866

chr19-29245435-G-Achr19-29245435-G-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 0.251 in 152,094 control chromosomes in the GnomAD database, including 5,060 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 0.25 (5060 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.251 AC: 38159 AN: 151976 Hom.: 5058 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.251 AC: 38167 AN: 152094 Hom.: 5060 Cov.: 33 AF XY: 0.253 AC XY: 18774 AN XY: 74338

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.236

Alfa AF: 0.255 Hom.: 805

Bravo AF: 0.247

Asia WGS AF: 0.344 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11083866; hg19: chr19-29736342;