rs1466308

Variant names:

• chr19-11845809-T-C
• rs1466308

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.487 AC: 20179 AN: 41416

American (AMR) AF: 0.351 AC: 5353 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3470

East Asian (EAS) AF: 0.153 AC: 786 AN: 5122

South Asian (SAS) AF: 0.263 AC: 1264 AN: 4802

European-Finnish (FIN) AF: 0.331 AC: 3486 AN: 10520

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27704 AN: 67942

Other (OTH) AF: 0.392 AC: 827 AN: 2108

Alfa AF: 0.402 Hom.: 2070

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
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1466308; hg19: chr19-11956624;