rs11086080

chr19-17816232-T-C

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 0.402 in 150,136 control chromosomes in the GnomAD database, including 12,578 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 0.40 (12578 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 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: 0.401 AC: 60237 AN: 150038 Hom.: 12552 Cov.: 28

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.402 AC: 60311 AN: 150136 Hom.: 12578 Cov.: 28 AF XY: 0.407 AC XY: 29758 AN XY: 73096

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.363

Alfa AF: 0.353 Hom.: 21318

Bravo AF: 0.407

Asia WGS AF: 0.536 AC: 1863 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.94
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11086080; hg19: chr19-17927041;