rs28678421

Variant names:

• chr11-1207775-A-G
• rs28678421

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 0.262 in 152,142 control chromosomes in the GnomAD database, including 5,801 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 0.26 (5801 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.262 AC: 39841 AN: 152024 Hom.: 5784 Cov.: 34

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.262 AC: 39899 AN: 152142 Hom.: 5801 Cov.: 34 AF XY: 0.261 AC XY: 19389 AN XY: 74372

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.267

Alfa AF: 0.227 Hom.: 4283

Bravo AF: 0.258

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28678421; hg19: chr11-1229005;