rs7219773

chr17-7379825-C-A

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 0.412 in 151,954 control chromosomes in the GnomAD database, including 13,258 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 0.41 (13258 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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: 0.412 AC: 62533 AN: 151834 Hom.: 13250 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.412 AC: 62565 AN: 151954 Hom.: 13258 Cov.: 31 AF XY: 0.407 AC XY: 30193 AN XY: 74268

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.392

Alfa AF: 0.444 Hom.: 31658

Bravo AF: 0.397

Asia WGS AF: 0.440 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.9
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7219773; hg19: chr17-7283144;