rs1466308

chr19-11845809-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 0.404 in 151,854 control chromosomes in the GnomAD database, including 12,792 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 (12792 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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: 0.404 AC: 61307 AN: 151744 Hom.: 12778 Cov.: 30

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.404 AC: 61357 AN: 151854 Hom.: 12792 Cov.: 30 AF XY: 0.396 AC XY: 29392 AN XY: 74208

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.392

Alfa AF: 0.399 Hom.: 1964

Bravo AF: 0.412

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.5
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466308; hg19: chr19-11956624;