rs7219027

Variant names:

• chr17-56745809-A-G
• rs7219027

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 0.267 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.222 AC: 9205 AN: 41512

American (AMR) AF: 0.280 AC: 4286 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.0919 AC: 476 AN: 5180

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4806

European-Finnish (FIN) AF: 0.249 AC: 2633 AN: 10578

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20731 AN: 67958

Other (OTH) AF: 0.278 AC: 586 AN: 2108

Alfa AF: 0.294 Hom.: 14874

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
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs7219027; hg19: chr17-54823170;