rs2543553

Variant names:

• chr17-7635645-C-A
• rs2543553

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 0.0566 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0149 AC: 621 AN: 41564

American (AMR) AF: 0.0638 AC: 975 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0181 AC: 87 AN: 4818

European-Finnish (FIN) AF: 0.0324 AC: 344 AN: 10624

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0866 AC: 5893 AN: 68012

Other (OTH) AF: 0.0743 AC: 157 AN: 2112

Alfa AF: 0.0841 Hom.: 811

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
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs2543553; hg19: chr17-7538963;