rs2543553

Positions:

• chr17-7635645-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 0.0566 in 152,286 control chromosomes in the GnomAD database, including 359 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 0.057 (359 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0566 AC: 8616 AN: 152168 Hom.: 358 Cov.: 31

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0638

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.0751

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

GnomAD4 genome AF: 0.0566 AC: 8615 AN: 152286 Hom.: 359 Cov.: 31 AF XY: 0.0529 AC XY: 3940 AN XY: 74464

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0181

Gnomad4 FIN AF: 0.0324

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0881 Hom.: 668

Bravo AF: 0.0588

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2543553; hg19: chr17-7538963;