rs4563545

Variant names:

• chr4-54744252-C-T
• rs4563545

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 0.271 in 151,978 control chromosomes in the GnomAD database, including 5,901 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 0.27 (5901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.271 AC: 41133 AN: 151860 Hom.: 5893 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.271 AC: 41151 AN: 151978 Hom.: 5901 Cov.: 32 AF XY: 0.264 AC XY: 19621 AN XY: 74286

African (AFR) AF: 0.356 AC: 14743 AN: 41418

American (AMR) AF: 0.322 AC: 4915 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1090 AN: 5176

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4812

European-Finnish (FIN) AF: 0.103 AC: 1086 AN: 10572

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16464 AN: 67948

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.260 Hom.: 709

Bravo AF: 0.295

Asia WGS AF: 0.233 AC: 810 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.61
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs4563545; hg19: chr4-55610418;