rs17560050

chr7-54060087-T-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 0.187 in 152,104 control chromosomes in the GnomAD database, including 3,113 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 0.19 (3113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.187 AC: 28493 AN: 151986 Hom.: 3109 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0578

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.187 AC: 28519 AN: 152104 Hom.: 3113 Cov.: 32 AF XY: 0.192 AC XY: 14292 AN XY: 74354

Gnomad4 AFR AF: 0.0970

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0579

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.158

Alfa AF: 0.216 Hom.: 3270

Bravo AF: 0.173

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.8
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17560050; hg19: chr7-54127780;