rs7219027

chr17-56745809-A-G

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 0.267 in 152,096 control chromosomes in the GnomAD database, including 5,629 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 0.27 (5629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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: 0.267 AC: 40548 AN: 151978 Hom.: 5624 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.0915

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.267 AC: 40583 AN: 152096 Hom.: 5629 Cov.: 31 AF XY: 0.262 AC XY: 19462 AN XY: 74370

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.0919

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.278

Alfa AF: 0.297 Hom.: 10128

Bravo AF: 0.272

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.6
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7219027; hg19: chr17-54823170;