rs1446682

Variant names:

• chr8-27219081-T-A
• rs1446682

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 0.188 in 152,000 control chromosomes in the GnomAD database, including 3,103 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 0.19 (3103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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: 0.188 AC: 28531 AN: 151882 Hom.: 3091 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.188 AC: 28556 AN: 152000 Hom.: 3103 Cov.: 32 AF XY: 0.190 AC XY: 14133 AN XY: 74278

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.205

Alfa AF: 0.222 Hom.: 498

Bravo AF: 0.172

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446682; hg19: chr8-27076598;