rs17560050

Variant names:

• chr7-54060087-T-G
• rs17560050

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 0.187 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0970 AC: 4028 AN: 41514

American (AMR) AF: 0.179 AC: 2740 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3470

East Asian (EAS) AF: 0.0579 AC: 299 AN: 5162

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3184 AN: 10560

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16076 AN: 67980

Other (OTH) AF: 0.158 AC: 334 AN: 2116

Alfa AF: 0.209 Hom.: 3947

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs17560050; hg19: chr7-54127780;