17-28415042-G-A

Variant names:

• chr17-28415042-G-A
• rs11080058

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 0.32 in 152,058 control chromosomes in the GnomAD database, including 8,105 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 0.32 (8105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48639 AN: 151940 Hom.: 8093 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.320 AC: 48674 AN: 152058 Hom.: 8105 Cov.: 32 AF XY: 0.320 AC XY: 23754 AN XY: 74306

African (AFR) AF: 0.391 AC: 16233 AN: 41474

American (AMR) AF: 0.377 AC: 5760 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1166 AN: 3464

East Asian (EAS) AF: 0.267 AC: 1385 AN: 5178

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4810

European-Finnish (FIN) AF: 0.232 AC: 2456 AN: 10566

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19217 AN: 67970

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.296 Hom.: 27843

Bravo AF: 0.333

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.041
DANN	Benign	0.50
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs11080058; hg19: chr17-26742060;